diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 4065 |
1 files changed, 2729 insertions, 1336 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe5ca9fbc7a..f3419900f5d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> @@ -55,10 +55,12 @@ #:use-module (gnu packages java) #:use-module (gnu packages javascript) #:use-module (gnu packages maths) + #:use-module (gnu packages ncurses) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) @@ -68,6 +70,134 @@ ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name "r-bsgenome-hsapiens-ucsc-hg38-masked") + (version "1.4.5") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version + 'annotation)) + (sha256 + (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m")))) + (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38 + r-genomeinfodb)) + (home-page + "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked") + (synopsis + "Full masked genomic sequences for Homo sapiens (UCSC version hg38)") + (description + "This package provides the complete genome sequences for Homo sapiens as +provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). +The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each +of them has the 4 following masks on top: + +@enumerate +@item the mask of assembly gaps (AGAPS mask); +@item the mask of intra-contig ambiguities (AMB mask); +@item the mask of repeats from @code{RepeatMasker} (RM mask); +@item the mask of repeats from Tandem Repeats Finder (TRF mask). +@end enumerate + +Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored +in @code{MaskedDNAString} objects.") + (license license:artistic2.0))) + +(define-public r-ensdb-hsapiens-v79 + (package + (name "r-ensdb-hsapiens-v79") + (version "2.99.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EnsDb.Hsapiens.v79" version + 'annotation)) + (sha256 + (base32 "0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg")))) + (properties `((upstream-name . "EnsDb.Hsapiens.v79"))) + (build-system r-build-system) + (propagated-inputs (list r-ensembldb)) + (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v79") + (synopsis "Ensembl based annotation package") + (description "This package exposes an annotation database generated from +Ensembl.") + (license license:artistic2.0))) + +(define-public r-hpo-db + (package + (name "r-hpo-db") + (version "0.99.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HPO.db" version + 'annotation)) + (sha256 + (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was")))) + (properties `((upstream-name . "HPO.db"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'avoid-internet-access + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cache (string-append #$output "/share/HPO.db/cache")) + (file (string-append cache "/118333"))) + (mkdir-p cache) + (copy-file #$(this-package-native-input "HPO.sqlite") file) + (substitute* "R/zzz.R" + (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };")) + (("dbfile <- ah.*" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \"" + file "\";} else { " m " }\n"))))))))) + (propagated-inputs + (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("HPO.sqlite" + ,(origin + (method url-fetch) + (uri "https://annotationhub.bioconductor.org/fetch/118333") + (file-name "HPO.sqlite") + (sha256 + (base32 "1wwdwf27iil0p41183qgygh2ifphhmlljjkgjm2h8sr25qycf0md")))))) + (home-page "https://bioconductor.org/packages/HPO.db") + (synopsis + "Annotation maps describing the entire Human Phenotype Ontology") + (description + "Human Phenotype Ontology (HPO) was developed to create a consistent +description of gene products with disease perspectives, and is essential for +supporting functional genomics in disease context. Accurate disease +descriptions can discover new relationships between genes and disease, and new +functions for previous uncharacteried genes and alleles.") + (license license:artistic2.0))) + +(define-public r-jaspar2020 + (package + (name "r-jaspar2020") + (version "0.99.10") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "JASPAR2020" version 'annotation)) + (sha256 + (base32 "0nrp63z7q2ivv5h87f7inpp2qll2dfgj4227l4rbnzii38a2vfdr")))) + (properties `((upstream-name . "JASPAR2020"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://jaspar.elixir.no/") + (synopsis "Data package for JASPAR database (version 2020)") + (description "Data package for JASPAR2020. To explore these databases, +utilize the TFBSTools package (version 1.23.1 or higher).") + (license license:gpl2))) + (define-public r-mafh5-gnomad-v3-1-2-grch38 (package (name "r-mafh5-gnomad-v3-1-2-grch38") @@ -98,6 +228,65 @@ It retrieves this data from the Genome Aggregation Database (@code{gnomAD} version 3.1.2) for the human genome version GRCh38.") (license license:artistic2.0))) +(define-public r-mpo-db + (package + (name "r-mpo-db") + (version "0.99.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MPO.db" version + 'annotation)) + (sha256 + (base32 "0x1rcikg189akbd71yh0p02482km9hry6i69s2srdf5mlgqficvl")))) + (properties `((upstream-name . "MPO.db"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'avoid-internet-access + (lambda* (#:key inputs #:allow-other-keys) + (let* ((cache (string-append #$output "/share/MPO.db/cache")) + (file (string-append cache "/118299"))) + (mkdir-p cache) + (copy-file #$(this-package-native-input "MPO.sqlite") file) + (substitute* "R/zzz.R" + (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") == \"\") { " m " };")) + (("dbfile <- ah.*" m) + (string-append + "if (Sys.getenv(\"NIX_BUILD_TOP\") != \"\") { dbfile <- \"" + file "\";} else { " m " }\n"))))))))) + (propagated-inputs + (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi)) + (native-inputs + `(("r-knitr" ,r-knitr) + ("MPO.sqlite" + ,(origin + (method url-fetch) + (uri "https://annotationhub.bioconductor.org/fetch/118299") + (file-name "MPO.sqlite") + (sha256 + (base32 "12rf5dpnjrpw55bgnbn68dni2g0p87nvs9c7mamqk0ayafs61zl0")))))) + (home-page "https://github.com/YuLab-SMU/MPO.db") + (synopsis "set of annotation maps describing the Mouse Phenotype Ontology") + (description + "This is the human disease ontology R package HDO.db, which provides the +semantic relationship between human diseases. Relying on the DOSE and +GO@code{SemSim} packages, this package can carry out disease enrichment and +semantic similarity analyses. Many biological studies are achieved through +mouse models, and a large number of data indicate the association between +genotypes and phenotypes or diseases. The study of model organisms can be +transformed into useful knowledge about normal human biology and disease to +facilitate treatment and early screening for diseases. Organism-specific +genotype-phenotypic associations can be applied to cross-species phenotypic +studies to clarify previously unknown phenotypic connections in other species. +Using the same principle to diseases can identify genetic associations and +even help to identify disease associations that are not obvious.") + (license license:artistic2.0))) + (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") @@ -395,6 +584,28 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-ecoli-ncbi-20080805 + (package + (name "r-bsgenome-ecoli-ncbi-20080805") + (version "1.3.1000") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version + 'annotation)) + (sha256 + (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27")))) + (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome)) + (home-page + "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805") + (synopsis "Escherichia coli full genomes") + (description + "This package provides Escherichia coli full genomes for several strains +as provided by NCBI on 2008/08/05 and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") @@ -809,13 +1020,13 @@ based on mapping using Entrez Gene identifiers.") (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") - (version "3.14.0") + (version "3.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) (sha256 (base32 - "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j")))) + "1jn556ql6xknfd34qz4bqh6bgc9rccmz6pk41p7ivlzlslz7bp21")))) (properties `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) @@ -957,6 +1168,46 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-escape + (package + (name "r-escape") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "escape" version)) + (sha256 + (base32 "0bmin69ax7l5x3a0k9mv183277a0hl4znx02y79v2ilkgqkdm7fn")))) + (properties `((upstream-name . "escape"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel + r-broom + r-data-table + r-dplyr + r-ggplot2 + r-ggridges + r-gseabase + r-gsva + r-matrix + r-matrixgenerics + r-msigdbr + r-patchwork + r-reshape2 + r-rlang + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/escape") + (synopsis "Single cell analysis platform for enrichment") + (description + "R-escape streamlines gene set enrichment analysis for single-cell RNA +sequencing. Using raw count information, Seurat objects, or +@code{SingleCellExperiment} format, users can perform and visualize GSEA +across individual cells.") + (license license:gpl2))) + (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") @@ -1463,6 +1714,26 @@ biscuiteer.") demonstrate functionalities of the @code{breakpointR} package.") (license license:expat))) +(define-public r-breastcancervdx + (package + (name "r-breastcancervdx") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "breastCancerVDX" version + 'experiment)) + (sha256 + (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0")))) + (properties `((upstream-name . "breastCancerVDX"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/breastCancerVDX") + (synopsis "Gene expression datasets") + (description + "This package is a collection of gene expression data from a breast +cancer study published in Wang et al. 2005 and Minn et al 2007.") + (license license:artistic2.0))) + (define-public r-celldex (package (name "r-celldex") @@ -1741,6 +2012,25 @@ package.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-jaspar2016 + (package + (name "r-jaspar2016") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "JASPAR2016" version 'experiment)) + (sha256 + (base32 "0dyx29f7jnyqcj85j2yrl8jcphi2kymx2y2mk7ws25xcahl5zzpy")))) + (properties `((upstream-name . "JASPAR2016"))) + (build-system r-build-system) + (home-page "https://jaspar.elixir.no/") + (synopsis "Data package for JASPAR 2016") + (description + "This is a data package for JASPAR 2016. To search this databases, +please use the package TFBSTools.") + (license license:gpl2))) + (define-public r-macrophage (package (name "r-macrophage") @@ -1764,6 +2054,34 @@ gene expression indicate a role for enhancer priming in immune response\", publi in Nature Genetics, January 2018.") (license license:gpl2+))) +(define-public r-methylclockdata + (package + (name "r-methylclockdata") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "methylclockData" version + 'experiment)) + (sha256 + (base32 "0q4hiclws0fg03kwvbdwka024gghl1hbmmfficxfghslll78mc3y")))) + (properties `((upstream-name . "methylclockData"))) + (build-system r-build-system) + (propagated-inputs (list r-experimenthub r-experimenthubdata)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/isglobal-brge/methylclockData") + (synopsis "Data for methylclock package") + (description + "This package contains a collection of 9 datasets, andrews and bakulski +cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, +combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, +guintivano dlpfc and saliva gse48472. The data are used to estimate cell +counts using Extrinsic epigenetic age acceleration (EEAA) method. It also +contains a collection of 12 datasets to use with @code{MethylClock} package to +estimate chronological and gestational DNA methylation with estimators to use +with different methylation clocks.") + (license license:expat))) + (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") @@ -1841,6 +2159,40 @@ LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example files for various search engines.") (license license:gpl2+))) +(define-public r-msexperiment + (package + (name "r-msexperiment") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsExperiment" version)) + (sha256 + (base32 "06m0i60zh3xjqmsz6dpp0il833xzdfj0fm6xbhl7kmicvfrcnyfg")))) + (properties `((upstream-name . "MsExperiment"))) + (build-system r-build-system) + (propagated-inputs (list r-iranges + r-protgenerics + r-qfeatures + r-s4vectors + r-spectra + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/MsExperiment") + (synopsis "Infrastructure for Mass Spectrometry experiments") + (description + "This package provides infrastructure to store and manage all aspects +related to a complete proteomics or metabolomics mass spectrometry (MS) +experiment. The @code{MsExperiment} package provides light-weight and +flexible containers for MS experiments building on the new MS infrastructure +provided by the Spectra, QFeatures and related packages. Along with raw data +representations, links to original data files and sample annotations, +additional metadata or annotations can also be stored within the +@code{MsExperiment} container. To guarantee maximum flexibility only minimal +constraints are put on the type and content of the data within the +containers.") + (license license:artistic2.0))) + (define-public r-msigdb (package (name "r-msigdb") @@ -2135,13 +2487,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0vrsyx06acdkb3hq350zdnx3bqzz43grf1w8n0pmxlcr2dncchv9")))) + "0p9q2x6n6n1d4w2hfbhhj54qflc6rf1w1qm9p2zqv9fcrm3g153v")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -2161,13 +2513,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1my2slp88qpb15qidjd646hlslvn8brv6i553h21c4c76jzxzsiz")))) + "0y8j66yargvipwxg2ffcs62idk5q5r8vracfldbd1x5rgq7lf6nq")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -2190,13 +2542,13 @@ ranking by fold-change and visualization.") (define-public r-adacgh2 (package (name "r-adacgh2") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 - (base32 "1mmckrxhv23kl3g4d3n4hfdm97sfg2k36khzy9i6d73g7c033hsv")))) + (base32 "0lzgn4zqckv37jsgd1azvshblb38khrlcncm98g74qhkswqj5wx3")))) (properties `((upstream-name . "ADaCGH2"))) (build-system r-build-system) (arguments @@ -2232,13 +2584,13 @@ storing data.") (define-public r-adam (package (name "r-adam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1hy7xdf6v2fqggvc9rdl90gn0l6vfbmvb23c61i8q45s3qsaxksp")))) + "0gz3mpkj1q4j7w08ylfzclpa6saxsz7wyp0cldllhxpcj9lxljs5")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -2267,13 +2619,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0jc0sbmmc98z75x73ns3qwcvklvx73wqla87cki8sls6ywa8w93j")))) + "10m5dplkzxsxm7dxcmybihv81yflm3f7q6fmgb1dvwr8lsn1dm03")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -2315,13 +2667,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0a3r4bkf6g28lgsq21077ag9ba6zrfv6yflawx9fg73zdx4266jp")))) + "0299yyin2j8577db2w6mrxmsq68cjlzwyh7z1wvhbj0n1p75r871")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -2364,13 +2716,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z")))) + "0av0kji4r788cn5808g13svqpydq6xk4d2awpzpsckz7xbjyx0ya")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -2392,13 +2744,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "0nf5dkidar6zp5rvpd7i19gdb7mnam9rmca3z3anxi0pdnalwc9d")))) + "1f508sz5vsmmmvp2mcyd2l4hislg2xhnn11xxva010l3i7by8c2r")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -2420,13 +2772,13 @@ expression values are known.") (define-public r-affyilm (package (name "r-affyilm") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyILM" version)) (sha256 - (base32 "02g0bg21ms0gmq6dvdcj91b0p47ppqcfvgj73y0mbdx6prrmcagx")))) + (base32 "1sbgc787gvcnpjhm0hv80rsms679wlvphq2ch7s28zdlaa2vz7sv")))) (properties `((upstream-name . "affyILM"))) (build-system r-build-system) (propagated-inputs @@ -2447,13 +2799,13 @@ concentrations on behal of the Langmuir model.") (define-public r-affylmgui (package (name "r-affylmgui") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affylmGUI" version)) (sha256 - (base32 "1m1gvz313h4x080889b05fjq60wn57dxlgq03qkwy65scl3x2fcn")))) + (base32 "1431zmh9van9605lh0i96as48zih17s3cfhjw94v37rswfq09fkg")))) (properties `((upstream-name . "affylmGUI"))) (build-system r-build-system) (propagated-inputs @@ -2479,13 +2831,13 @@ limma packages.") (define-public r-affyplm (package (name "r-affyplm") - (version "1.76.1") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyPLM" version)) (sha256 - (base32 "1660nn4541f2k5qpzxkkkf9h92ndzqr0j1jpzh4czs466766kn8y")))) + (base32 "0l7rfwj1bdkk9vd5j0zby2ijpapmd5k0s6l84zy4ld47vabxyaa6")))) (properties `((upstream-name . "affyPLM"))) (build-system r-build-system) (inputs (list zlib)) @@ -2510,13 +2862,13 @@ also provided.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "14s3kvxcc3qj931bf5ya088flijmn5z89hps3di98kkdsl3w6d4g")))) + "0i7929cyqvbx81v1d629g53480m48cbdpxfv0k6lwjfzf4yvazhf")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -2535,13 +2887,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0p9qmwhi4ik24m51cvgxnny4yfqv4v0rvra16bj5d3w9bw9yf3an")))) + "06z74p3khw3r8dnwrpyyikq3ifcdvffxgfwcic9j8vc9s8pf921s")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -2562,13 +2914,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0g7n6dj1scad833y2182946hn3yh4jad20wvw9ic8gmqb438vihj")))) + "1i04hhncz9lhjp730gyknd8v7zakz1whc2a5pw3pn37h8k9mq5la")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -2596,13 +2948,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.32.0") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "0rm646iqc8hf8vfk0pdg064hm9k4k371bp1q4k7z2l16zhs8a07r")))) + "0xbbcmnbnj7y3a1wndv6zhqhrwdpdj6207wh4n0qz794akciw84a")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -2618,13 +2970,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "17cm65n2awbwmk5i8h1n30abk6pww42ngcy9m24dxz1qdbnvx5fn")))) + "0fb670gxzl5aq6vmb5d2l04r0408gxrqs06k1a3b3pzkdbd7qxwm")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs @@ -2663,13 +3015,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "1gydc2sy0lf2h83dzr60w9k3ipqd8h62q6764xpn31girwx70rdz")))) + "0cimi60asz5mmrq2qmnyqq9x5yg14cc67j8135x9zlklblsfyf35")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -2693,13 +3045,13 @@ objects are used so that other packages could be used as well.") (define-public r-aims (package (name "r-aims") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "1mbwv70ypkb3x086css94m89wq9pqzd23i7nar1844vbqpw3j83q")))) + "0fmzyd8vypcfadqfa8w11mxr12h4a9shgiqpi2n2y150fvhlqf6c")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) @@ -2717,13 +3069,13 @@ well as on dataset of gene expression data.") (define-public r-airpart (package (name "r-airpart") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "024vcxf23irlysc8srqii3zqhhldpwdcj0i4zzhz18x3bdy9cbj0")))) + "1bdlg078nlpibbn3y1cbkglhlm440crx3alzhv9k0psv6arg2kqb")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs @@ -2764,13 +3116,13 @@ datasets.") (define-public r-amountain (package (name "r-amountain") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj")))) + "1c65vn2k3hzzymik9ia7nk32sf0hr83q27yzf561a1hgv3m67d65")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -2788,13 +3140,13 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amplican (package (name "r-amplican") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "amplican" version)) (sha256 (base32 - "1bws4awpjvswzj53zwn9x5ra76ngpqn2h8hlr6y0x7j9wwwqldc7")))) + "0xsw6226yyyl5zgmcyfim6dxj04zrpzbd1288l0hysq1s3b1yslw")))) (properties `((upstream-name . "amplican"))) (build-system r-build-system) (propagated-inputs @@ -2835,13 +3187,13 @@ problems.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f")))) + "1h0ci2sak2x5dhcshmgk4hy53ggjvrz3kaj61m47w5fjkj0lz79s")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -2887,13 +3239,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "0f2xc0pm7ld72fnmqirr0q2a5xfh12cag6s2yysblslh9ajyzcmw")))) + "1f2xf1i9l1s7433mvqjsralpm77qg0m73dw1rq9jsxbpk1f502ld")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -2917,13 +3269,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "0jws3wqgwc0gnp7smc0lsqfw9jbcik36pl7vz9a8ndgwpp9c8653")))) + "1m63k1b9xh5mv4zb5m9nlrdcqkh2h477x1zyfk8j89idcvk9jil7")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -2966,19 +3318,18 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.16.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "1z46lpd2zi3b88i27qm48wy4acb2xsjh63zgxhfx2y4bgvr29ni7")))) + "1q0ca3pagqzj12kah79jg4py3ibz7qsdl975r2mxhphqwj76gnh8")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs (list r-ape r-assertthat - r-biomformat r-caret r-covr r-deseq2 @@ -2986,7 +3337,6 @@ these biases and construct statistically consistent estimators.") r-dt r-forcats r-ggplot2 - r-glmnet r-gunifrac r-lattice r-limma @@ -2994,9 +3344,9 @@ these biases and construct statistically consistent estimators.") r-matrix r-multiassayexperiment r-plotly - r-plotroc r-rentrez r-reshape2 + r-rocit r-s4vectors r-scales r-shiny @@ -3025,13 +3375,13 @@ to understand their data better and discover new insights.") (define-public r-annotationhubdata (package (name "r-annotationhubdata") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHubData" version)) (sha256 - (base32 "109gi5cs82j135q00wg9dfx0z5m9bs1kc7s246ym13ik43z0h3qq")))) + (base32 "0jkz65z7l9vaxid6vpsr4rdavarkayfrgkybzhwf9va82jsnkd3z")))) (properties `((upstream-name . "AnnotationHubData"))) (build-system r-build-system) (arguments @@ -3076,13 +3426,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.12.4") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "05wgrr16vaqb7982j7nyri6rrhx90ljgxc37afhw190wc5dj07n0")))) + "06n0as71m3dfbnzjfq8f1s0r40w4flc8am7zb0293c1037clmcig")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs @@ -3117,19 +3467,22 @@ to transform JSON responses to formats more amenable to manipulation in R.") (define-public r-aldex2 (package (name "r-aldex2") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8")))) + "0wchlw9dprw7vkw26h26ypx06xv2j0cxbidw61pcqaxmrrh14dhz")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel + r-directlabels r-genomicranges r-iranges + r-lattice + r-latticeextra r-multtest r-rfast r-s4vectors @@ -3158,13 +3511,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "137bvqyh1cqmhf9x3xl6n1dv0380lpcr2nxhd60b7zqiw4p14i5a")))) + "0lhbh9xgkbrad9fqvxl4c6y0f2kgibn6sinp8znysk5m9z0ngpwp")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs @@ -3192,13 +3545,13 @@ generated as HTML or PDF files, or as Shiny applications.") (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "11431d453xszzjyxr10npnblhlrfw8hl5jgabpxla7cj77w02wnr")))) + "0zja8mysw0ljkvk6vqdx4c9wpf45zs64iyazh90mlf6xhbrvqfvq")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs @@ -3272,13 +3625,13 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "0rp82y7163pjbl7n6fyywh4l0sgzn1z8kp83v0kg7xk3810mj9sm")))) + "0141kayx20mm8skqr2210bpl76ra560ik7gf71iar03r3izcfczq")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs @@ -3326,13 +3679,13 @@ data. Efficient plotting with 1-D data is also available. Basic reading of (define-public r-altcdfenvs (package (name "r-altcdfenvs") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "altcdfenvs" version)) (sha256 (base32 - "1jpimj195rdw86pp623ylrmcxkxmn8qmc84vsw9prnf3gdz3q18b")))) + "17kgiqa5dbfp74jrm565wlx9sj4ydbds2y8ahs7dikvdvm725qsn")))) (properties `((upstream-name . "altcdfenvs"))) (build-system r-build-system) (propagated-inputs @@ -3357,37 +3710,37 @@ create an alternative mapping from sequences.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1l33yb20pynkvlla1dmgbwjhnhxh067fci0ciryxmbzqwq2sn1kc")))) + "0x7v60j1c1g12qlqxgshpmbnwzjbmlnkrfh60wl43inr0wyllq1l")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs - (list r-genomicranges - r-aneufinderdata + (list r-aneufinderdata + r-bamsignals + r-biocgenerics + r-biostrings + r-cowplot + r-dnacopy + r-doparallel r-ecp r-foreach - r-doparallel - r-biocgenerics - r-s4vectors r-genomeinfodb - r-iranges - r-rsamtools - r-bamsignals - r-dnacopy - r-biostrings r-genomicalignments - r-ggplot2 - r-reshape2 + r-genomicranges r-ggdendro + r-ggplot2 r-ggrepel + r-iranges r-mclust - r-cowplot)) + r-reshape2 + r-rsamtools + r-s4vectors)) (home-page "https://bioconductor.org/packages/AneuFinder/") (synopsis "Copy number variation analysis in single-cell-sequencing data") (description "This package implements functions for copy number variant @@ -3426,13 +3779,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "0gilb8yxba1cqi678w9xkq77m8lf3k8dqcldh68cll61xsgihl1v")))) + "1gf0qdhj4ijgb6b67fh94zx084k5r87la3d7vc0qxs413rvr4mj8")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs @@ -3460,13 +3813,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "0ix0r36fs6vr0gyryi1j15pcc0hvpynsg9505w95dsn3p4fdnhg8")))) + "14lzyq08gnm9r99xwaqh50sz0dwzhmiyyylkg239dlbw80zmv404")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -3486,13 +3839,13 @@ tumor samples from healthy controls.") (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "1ib33fw379sakk084csa3pwcc3wvba38ily6mmv2ax1wh16i0pfz")))) + "0cnb6r6rqbz5qph32aa1mghr0w2rhl6znyiblj0cbkv45mx2k4jr")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs @@ -3513,13 +3866,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (define-public r-arrayqualitymetrics (package (name "r-arrayqualitymetrics") - (version "3.56.0") + (version "3.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQualityMetrics" version)) (sha256 (base32 - "06plgmgla7hvryqfcid4y35s24r50s39d9f8sjchwbxqciwy72wj")))) + "1k80ih7r3hf48r9rp9dl2wl8m17620dqr4fch49kdsq97hm5q5dm")))) (properties `((upstream-name . "arrayQualityMetrics"))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -3551,13 +3904,13 @@ supported.") (define-public r-arraymvout (package (name "r-arraymvout") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayMvout" version)) (sha256 - (base32 "1wdqcfa0h070lky4m2h5k4wg8lg7014y0gk95gip5zags29zjwqb")))) + (base32 "0z3ksx0yigan5aiq7vsdx78khlrcdxa4yd5b46rfn83gsrjbxzhz")))) (properties `((upstream-name . "arrayMvout"))) (build-system r-build-system) (arguments @@ -3587,13 +3940,13 @@ fixed Type I error rate.") (define-public r-arrayquality (package (name "r-arrayquality") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "arrayQuality" version)) (sha256 - (base32 "0lq59y4pi13z4v1i1ah78xlchxy34x1lplsh0n42wlk88rk0rqxd")))) + (base32 "1bm46zf5c1i7fd848bqajv3agl05b93xsvam7034033ypyx6bf1z")))) (properties `((upstream-name . "arrayQuality"))) (build-system r-build-system) (propagated-inputs @@ -3612,13 +3965,13 @@ quality assessment.") (define-public r-asafe (package (name "r-asafe") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "05xw42552x7by63psb05hvjraax66flg94i331ca61zx107q7fai")))) + "13pn2s59npp8lhc2sk9sa7dq8fy6jlq22c71n3rcjgxrrh690nb8")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3635,13 +3988,13 @@ pairs.") (define-public r-aseb (package (name "r-aseb") - (version "1.44.0") + (version "1.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1dq6b5rg9iw6hdjmd7g0w64z7cxm52yg1cjyv355qs064dx26nph")))) + "1da6ld3ij55l3saj05ink8i1f6gqwyrv896qh8g94dmh6vzn2xbr")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -3662,13 +4015,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "0vb37rvrb08qvv0i2k9jnqpajzpj044ww05w3kq1kypbby0c84zs")))) + "13nk19rccrp0xl1s5gjwydpl1ayc7zc2izjrij9iz7fh2r79gn7f")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) @@ -3685,13 +4038,13 @@ model as latent variables.") (define-public r-asics (package (name "r-asics") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASICS" version)) (sha256 (base32 - "0svl9wnfn9z88j1yyl30b1f3d14h01x4cga8q04x530723xnjws7")))) + "10wlmnlpn6ji256fp81rhsm2rsbsqsbvbjqqpw9vib11cwpam9wd")))) (properties `((upstream-name . "ASICS"))) (build-system r-build-system) (propagated-inputs @@ -3719,13 +4072,13 @@ the spectra of the library with a sparse penalty.") (define-public r-aspli (package (name "r-aspli") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "0462hf7anpmmqq4585kmjilw1q229r38lijbxq8xg0f3m8xvr1ga")))) + "0rj103vvff2c20r018491i71393x0idq22ri4zg3qibx2accd7jy")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs @@ -3767,13 +4120,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "16nv6sh7z3l6ff3a7zrixkc04mhrak38q045xlirgljkcragz1c5")))) + "0v64d3nmvcj6bz8zplyqzslm7kz6j3y0nl316h76g094hify64lk")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs @@ -3796,13 +4149,13 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "1vksbfd4wd2xcc0nl3wp53vm0jyqy97p0hqps2aml04745vkg023")))) + "0mm15i59vsnz8zh2d10xnab3a6kq08hwd3pzm3r12g4wcrdsxfxc")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) @@ -3823,13 +4176,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "1057mkxrjfnqhb1mydhd7vlb1s8h7n4zc4cl063gw4sgj6mw99ij")))) + "1qfgy76d65hbx32fw1yf20n1vavylcafb9fgqqp02r455vk3xzng")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -3864,13 +4217,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "14j8lbry4wpn8izch1nra5npg4qsh49ql4bf21jvvr3gl3qa1g7l")))) + "1nksx6al1cr6apknvrabi3gdbr7m61ms81nmkq4qykx5aysmp8mv")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs @@ -3897,13 +4250,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "1lb6npxm5f82z8278v6fh7k5w8d4z73881iplm3ashc27wiw6sz3")))) + "0lk8gfbccrxly7gn629497sxz0mj3m9wcwdahqv1m7l6fjnf5563")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs @@ -3928,13 +4281,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x")))) + "10c5qi040z2w46k7qdcd2yap11mzllllrbr0nx7gd9gfzwlx089s")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs @@ -3952,13 +4305,13 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji")))) + "0hry7ynv69hqbwyhlsilf1f9w8yadidbn2ckm5dx9mnb5ihgkyvj")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -3979,13 +4332,13 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "0bp8p7cn59iv08cf4yw9xl1f83dcr6v1kqvggxjals8y4gmls9nz")))) + "0d08mp12lw4qdy7w7i474ywcy2zgv940nc44w0gbb9h9dfl22crv")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl @@ -4016,16 +4369,37 @@ BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.") (license license:artistic2.0))) +(define-public r-bags + (package + (name "r-bags") + (version "2.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BAGS" version)) + (sha256 + (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh")))) + (properties `((upstream-name . "BAGS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-breastcancervdx)) + (home-page "https://bioconductor.org/packages/BAGS") + (synopsis "Bayesian approach for geneset selection") + (description + "This R package is providing functions to perform geneset significance +analysis over simple cross-sectional data between 2 and 5 phenotypes of +interest.") + (license license:artistic2.0))) + (define-public r-basespacer (package (name "r-basespacer") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "15aqf2s51gl6gcnv24170v9hlq1vgya58qh1f5vjmark7j2k8vvm")))) + "1ldsgrhxb1nm8xj7mws461apjknp9c2bhq3738f63i2qj9g25j4g")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) @@ -4066,13 +4440,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "0g3yvgrarpdcxpvjrxg0gbdcagknh80cr0xyzinzpmiiz0rywmzc")))) + "0zmf7a7lwsnk9gcg48vmzdvfmzhvnbawwg77pb4gy3cw9sjdz5ym")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") @@ -4090,13 +4464,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "04bzb3i461gwkq9ygkjljpjk32c3arqr08hfzxyig1sarrryzl3q")))) + "17smlghl8s667n6cjx64mqli9drmv0pkq51mhjlyjy2v019im7l9")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs @@ -4117,13 +4491,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.2.6") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0h7ps32vbcn4hjpfb343nn8b50zq9my0k61847fi69vc4siwcx5k")))) + "02pcab8jfwlx4y00yky63anba61bb1h884m0f6ajvasfpgl30w6i")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -4160,13 +4534,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.16.1") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "04l6iy0sij7zhzswhxjzir3xmrjnp6aapp0a93xp01xiv2sgdzni")))) + "0y81m37c5irpaw9pfm5b672wk804n4x1g9g5pfh1dp7pggfwbf1z")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4198,13 +4572,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y")))) + "0y6mizkbx3s2x6465g53q87q0sixxrxhjvjmvwiilhirxf4x7hgp")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs @@ -4226,13 +4600,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8")))) + "1w5p6dqagf3g27ymqsxdim0qhnwm11rrs3nnpp4mj8jcxm8wjsh9")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs @@ -4268,14 +4642,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.17.1") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0n29adnb62agp9li8rmn68z653d2m41iy9zjz75h43a05drlgp33")))) + "15wr651ylbx3am213dsy5kdr1xc8r5c9rfq5ydxzqlmxzjgymj55")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -4288,13 +4662,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.46.0") + (version "0.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "19kwpis282i8x31xlh8nc3z6vvn23p3wpx7wmrqhclf8ymq61c7z")))) + "0av525j9l0y3kjdy5wl6s35sh4nsabmdclq3687l5258kmq2dq8k")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -4308,13 +4682,13 @@ packages.") (define-public r-breakpointr (package (name "r-breakpointr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointR" version)) (sha256 (base32 - "001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n")))) + "1jhgimybc2ib201k6vs5nfyi1whpkkzn7nj562yhz74208fx793a")))) (properties `((upstream-name . "breakpointR"))) (build-system r-build-system) (propagated-inputs @@ -4342,13 +4716,13 @@ export of Strand-seq data.") (define-public r-cardelino (package (name "r-cardelino") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cardelino" version)) (sha256 (base32 - "0ivhqd3da23iy2qklk2nljkjjr943m9r2y1q51fphld33izmv64v")))) + "0y4d3db01jwahz01hx3dswc4gg0x5k7325v4n1illgw3ddj2mvgn")))) (properties `((upstream-name . "cardelino"))) (build-system r-build-system) (propagated-inputs (list r-combinat @@ -4380,20 +4754,20 @@ stochastic dropout events as well as systematic allelic imbalance is used.") (define-public r-cellid (package (name "r-cellid") - (version "1.8.1") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CelliD" version)) (sha256 (base32 - "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) + "13hwxhdp268h3n8d8wgr75i60apa9mama9bg049yz7c6mj5ixd1v")))) (properties `((upstream-name . "CelliD"))) (build-system r-build-system) (propagated-inputs - (list r-data-table - r-biocparallel + (list r-biocparallel + r-data-table r-fastmatch - r-fgsea + r-fgsea r-ggplot2 r-glue r-irlba @@ -4404,13 +4778,14 @@ stochastic dropout events as well as systematic allelic imbalance is used.") r-rcpparmadillo r-reticulate r-rtsne + r-scater r-seurat + r-singlecellexperiment r-stringr - r-tictoc - r-singlecellexperiment r-summarizedexperiment + r-tictoc r-umap)) - (native-inputs (list r-knitr r-scater)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/CelliD") (synopsis "Single cell gene signature extraction using multiple correspondence analysis") @@ -4425,13 +4800,13 @@ enrichment in single cell data.") (define-public r-coregx (package (name "r-coregx") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoreGx" version)) (sha256 - (base32 "09pv117g8sxhrij960mparrz1r9vx8s20gmpvn1h667kl1bc0jm9")))) + (base32 "0ffbi5afw759mi5r657h67hdh9yr5jrzvl3aigp960jzb5542105")))) (properties `((upstream-name . "CoreGx"))) (build-system r-build-system) (propagated-inputs @@ -4470,21 +4845,21 @@ the curve} or @acronym{SF, survival fraction} are included.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1ci07y75nvvv1mxy23v6jp5xb6n023fvlqh9il5lsdqwyfl5nz9s")))) + "1sj1vr84nsbygkh5mmp7zm21zzk4zcw3bwcvcazmy54zs553blpf")))) (build-system r-build-system) (propagated-inputs - (list r-s4vectors - r-iranges + (list r-genomicalignments r-genomicranges - r-genomicalignments + r-iranges + r-rsamtools r-rtracklayer - r-rsamtools)) + r-s4vectors)) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of @@ -4497,13 +4872,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1xin1azby96xxp4yyd4wc3rfcjc2g9p01ksfd89bk2vxcclccqxn")))) + "1a5x3jzagd1a385yk1brs4say02r0l21qqjak4cl6fsv8ihhy05s")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -4527,13 +4902,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "0z4y57hna312pkhkchair8calm7wl40rx8lcm8i6h1789hba063d")))) + "1ckk8h6adylaxq6bh14ym9vvrrhsfglnaigqz16v96vsj8q9i336")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) @@ -4549,13 +4924,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd")))) + "0mbm884dm30b4fwf3qr1w96j18dxdmr2bn11dw83hh0wrbhp8njm")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -4590,14 +4965,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "12ld1f3892ag1a3lmkwjlkk6pd79ibykg8jrmddx2x33k23cv67g")))) + "1ldxw457zsfphm6izxz2kvxy3719gszhxb8mymx8njg6islljy27")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -4629,13 +5004,13 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh")) + "1swqqrlwin2i2qq46qyfziblbfsfyd5hf6w39hygp7fdkpic14b7")) (snippet '(for-each delete-file '("inst/java/CornerDetect.jar" @@ -4644,9 +5019,6 @@ set analyses, and can deal with repeated or longitudinal data.") (build-system r-build-system) (arguments (list - ;; XXX: since the upgrade to R 4.3.0 this package takes too long to be - ;; loaded. - #:tests? #false #:configure-flags '(list "--fake") #:modules '((guix build r-build-system) @@ -4674,7 +5046,7 @@ set analyses, and can deal with repeated or longitudinal data.") (add-after 'install 'strip-jar-timestamps (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) (inputs - (list (list icedtea "jdk") + (list (list openjdk11 "jdk") java-pj)) (propagated-inputs (list r-apcluster @@ -4706,13 +5078,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n")))) + "1ri8ldx3dqcpfvn3mz0022f77zi6ki04mh27qp132bbrjkj6zl79")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -4805,13 +5177,13 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "028sczy1d108i05ymr1wpj6jdrcds476wbmmc7rzzflzyg4aix75")))) + "13vwrg82zprb9h72azdqd0rkm5k2xm4mw7viawbzwkkqvg6azsdj")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl @@ -4848,13 +5220,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "0bmkyci31p7g097i8fvc0s1fz47hv6vp5rcfqqkvclm86wfkkmkc")))) + "1k5xrx97w9g0jfvjzawyfsqyz2fj9r463nj849djxgmcw8vp53vg")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs @@ -4875,13 +5247,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "08niwixy4m6gqmazisxzbbla9nsxicpa685jy3r6knapwaznvcb2")))) + "0m4zd6qxsrp7w9a8psg8xcrviim6plwgwn4rgdxy8ag0c442fsvk")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs @@ -4901,13 +5273,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1r5js5prwy1libnf1g1a4pdi15pj216bb8ajhzii3symn5r0cdj9")))) + "0pl4nwaf8swwz9nl2ynf9mm38d0x223gpz89qrj03yihxszy2n13")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -4946,13 +5318,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "012d76jwgg6fwfjc00zdws59y6jbj0grzd4lgjrqs2afp2ycmh9s")))) + (base32 "1vnlrkza33nb80qf810yfz66m3j84p8chhfdxak5lvpciqwx7dh9")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs @@ -4987,13 +5359,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "11cnyy3hyn8akhmax25293mx2blcs8ba5vfax6mx6hjhb577hkwb")))) + "16dkjqy9ba5v8nikaxdjcz7rr60dg46sfsgrjjlp82rf3256bf8r")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -5023,13 +5395,13 @@ bases such as COSMIC.") (define-public r-degreport (package (name "r-degreport") - (version "1.36.0") + (version "1.38.5") (source (origin (method url-fetch) (uri (bioconductor-uri "DEGreport" version)) (sha256 (base32 - "15xm1l2qgsyzaw820a1fq5qdzh5pj4dmr1hx6s6b6wm2p02cvvai")) + "0s0d40ac1da73w7j96lb20wchgs4c2svfrafsgi9mx5hiswfz25z")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "DEGreport"))) @@ -5052,6 +5424,7 @@ bases such as COSMIC.") r-complexheatmap r-consensusclusterplus r-cowplot + r-dendextend r-deseq2 r-dplyr r-edger @@ -5067,6 +5440,7 @@ bases such as COSMIC.") r-rlang r-s4vectors r-scales + r-stringi r-stringr r-summarizedexperiment r-tibble @@ -5094,13 +5468,13 @@ fold changes mean and variability for each selected gene.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.26.7") + (version "0.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1xsq85nm1gk537mw6ppsyykpw70kczv6wn1nll63b0k8xs4wj0ha")))) + "0mf30vdns64mpm11zcz9qx6nh5clr6krjvcmr7dqv2xg5ig0a1f7")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -5110,7 +5484,8 @@ fold changes mean and variability for each selected gene.") r-matrix r-matrixgenerics r-s4arrays - r-s4vectors)) + r-s4vectors + r-sparsearray)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") @@ -5128,17 +5503,21 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-densvis (package (name "r-densvis") - (version "1.10.3") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "densvis" version)) (sha256 (base32 - "1nkii02bj49z9qm3rj8lzwpz7dllrsa5zf7dn5ffcczyxr3b1ap9")))) + "11a112r2ckzphqj3r3fxvablzwgri0j5lx3ggh1z6pfnv113xxwj")))) (properties `((upstream-name . "densvis"))) (build-system r-build-system) - (propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp - r-reticulate)) + (propagated-inputs (list r-assertthat + r-basilisk + r-irlba + r-rcpp + r-reticulate + r-rtsne)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/densvis") (synopsis @@ -5159,13 +5538,13 @@ heterogeneity in the original high-dimensional space.") (define-public r-derfinder (package (name "r-derfinder") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinder" version)) (sha256 (base32 - "1gb65hk26ffn0njsgwgk43z9i9bcvx89pz5m9x951c2a07c1xrcw")))) + "0rj3szlpbxiwj3rajmr6ccnbs1mkcskql12iip8zgswmhz76rxh1")))) (properties `((upstream-name . "derfinder"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -5205,13 +5584,13 @@ The DER Finder approach can also be used to identify differentially bounded (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0ww4lvwmm8rf44wgksg98bqh7zlm503c4gc8dwilb1w0dz2k7qll")))) + (base32 "01vq8xnszxqhijranzaciapw8mcn6px0jhx9zb9lyqhsvaffjh5r")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -5230,19 +5609,18 @@ calculation in parallel.") (define-public r-dmrcate (package (name "r-dmrcate") - (version "2.14.1") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DMRcate" version)) (sha256 (base32 - "1va60r297cl6xw5mc4nf9igfizqqzz7i5436x26iw4q35jcwlfjl")))) + "19dxpmjjg8v2l71yjjlfj0ycvmhi9rk04q59nwjcp0aw8nvk6l3w")))) (properties `((upstream-name . "DMRcate"))) (build-system r-build-system) (propagated-inputs (list r-biomart r-bsseq - r-dss r-edger r-experimenthub r-genomeinfodb @@ -5271,13 +5649,13 @@ possibly confounded by SNPs and cross-hybridisation. It includes (define-public r-drimseq (package (name "r-drimseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98")))) + (base32 "1nf044cfqywfnglm081xbppamva87z2j2xz0f51z8mra11apj6i6")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -5306,13 +5684,13 @@ results.") (define-public r-dropletutils (package (name "r-dropletutils") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DropletUtils" version)) (sha256 - (base32 "09xwfb4ihpsp465vb1zbcwm6ww6qi3spn9d8p4i1gczyc0p9pf1y")))) + (base32 "0bnxk72a0ygh4nqwyjzzi79zc4md8pwk0pr6jn43in0wdk054wf6")))) (properties `((upstream-name . "DropletUtils"))) (build-system r-build-system) (propagated-inputs @@ -5347,16 +5725,45 @@ identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-limma from Bioconductor. +(define-public r-dsb + (package + (name "r-dsb") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dsb" version)) + (sha256 + (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) + (properties `((upstream-name . "dsb"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-magrittr r-mclust)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://github.com/niaid/dsb") + (synopsis + "Normalize & denoise droplet single cell protein data (CITE-Seq)") + (description + "R-dsb improves protein expression analysis in droplet-based single-cell +studies. The package specifically addresses noise in raw protein UMI counts +from methods like CITE-seq. It identifies and removes two main sources of +noise—protein-specific noise from unbound antibodies and droplet/cell-specific +noise. The package is applicable to various methods, including CITE-seq, +REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette +for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb +in Python.") + (license license:cc0))) + (define-public r-dss (package (name "r-dss") - (version "2.48.0") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 - "1aslbzwqfp609ym98k6cjjf6r1ns9hxcpx4igfjhqf2v0pazz2q8")))) + "1wjd428kz2w3n4ak13h3i1yknm03fh911jrcy2hkcip4z5cssla0")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) @@ -5376,13 +5783,13 @@ Beta-Binomial distributions.") (define-public r-dyndoc (package (name "r-dyndoc") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 - "16cb4pby6ja0xy8ygbgr6zfbyp4agyhlds5sayc5ryq50vafykah")))) + "0d2axaszy7rpi47yg4vhd1z70m53nx40znapgg5pq6ahrx7if5f1")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") @@ -5395,13 +5802,13 @@ dynamic documents and vignettes.") (define-public r-bluster (package (name "r-bluster") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "15f103lpl686730vl8g69fhki9iq2ncgr5dm6qm2xc9bq9vh65s9")))) + "16zkv567d39258syhfb215y04sq3pnfjh9pgbp5z85hcfpz4qmhc")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -5425,21 +5832,21 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.36.0") + (version "1.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1za1cxf734mar9hbvqrijdg61g0jag9jdzmi8p8ka62xbikxqa3s")))) + "1bhari5ghag5f5dlrgm79hckbh0bamd9567z04qi0spnfr97wf3s")))) (build-system r-build-system) (propagated-inputs (list r-biobase - r-iranges + r-genomeinfodb r-genomicranges + r-iranges r-rcolorbrewer - r-rtracklayer - r-genomeinfodb)) + r-rtracklayer)) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with @@ -5449,14 +5856,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "19fk4pzhwj9pfh4vg943xb4cdfpq65ax75d61w1mm3f71gg56z5g")))) + "1d9in3hs2n91pv498715d3qi82c7xsnm42vnzgfyz096zjghgp7a")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -5488,8 +5895,8 @@ arbitrary genomic intervals along chromosomal ideogram.") r-rcolorbrewer r-reshape2 r-rjags - r-singlecellexperiment r-seurat + r-singlecellexperiment r-summarizedexperiment r-tidyr)) (native-inputs (list r-knitr)) @@ -5509,13 +5916,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.34.1") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z")))) + "0rhh82hrsm32bdjamfah84p7zi8fvr4shyq2rdjfxzdp9qy5rh2q")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -5537,13 +5944,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "2.0.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "1zjwhxlayz2sb77vspw280didhawj282i5gvxnydcdparg165zwf")))) + (base32 "1yin2jv06g3jrzadq6yjcr14jz1zzwyxipzna5csgr013dkkrl8h")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -5618,13 +6025,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") (define-public r-italics (package (name "r-italics") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 - (base32 "09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08")))) + (base32 "0zk9n94nqw6vpw908ka32zppxwqkki9krzxib06y1nic3bri3w9i")))) (properties `((upstream-name . "ITALICS"))) (build-system r-build-system) (propagated-inputs @@ -5753,13 +6160,13 @@ mapping.") (define-public r-nebulosa (package (name "r-nebulosa") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Nebulosa" version)) (sha256 (base32 - "0lqm9mfmaxdhhs9di2kjg2rixng78lrrikyp7blmpyqk4c41j3nh")))) + "0kzkdwxrhl7plbcbqr58gnadhhbhx2811ian0s4kds14y4mxl26c")))) (properties `((upstream-name . "Nebulosa"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 @@ -5781,6 +6188,52 @@ multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment} objects can be used within Nebulosa.") (license license:gpl3))) +;; This is a CRAN package but it requires r-rcy3, a Bioconductor package. +(define-public r-netgsa + (package + (name "r-netgsa") + (version "4.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "netgsa" version)) + (sha256 + (base32 "1m9myxsbvbljr038azxzakpbh20a21qhiy20d0ipvjc5asq3kfla")))) + (properties `((upstream-name . "netgsa"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-corpcor + r-data-table + r-dplyr + r-genefilter + r-glassofast + r-glmnet + r-graph + r-graphite + r-httr + r-igraph + r-magrittr + r-matrix + r-msigdbr + r-org-hs-eg-db + r-quadprog + r-rcpp + r-rcppeigen + r-rcy3 + r-reshape2 + r-rlang)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikehellstern/netgsa") + (synopsis "Network-Based gene set analysis") + (description + "This package lets you carry out network-based gene set analysis by +incorporating external information about interactions among genes, as well as +novel interactions learned from data. It implements methods described in +Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, +Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, +Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.") + (license license:gpl3+))) + ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package @@ -5829,14 +6282,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.78.2") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0zsr87zsw5rp5rgdiv1bbsi6fx6b7qzlgjirzczky6fmf4dqwgnm")))) + "0lsvcv7nprmsh62d0r2v44a5n915crvv1cbj9ba6fdggj7wp8zyk")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -5857,14 +6310,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.76.1") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0wccj8q8sl0zc68nr5qf1qih8awqf1h6bwi5hq9d7r59p4g4r9n1")))) + "0818mgwny9hznw7lawrvmk11nwy0wxgjnlkf083vv3js4aq31gfp")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -5923,14 +6376,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "07a6kd51rlj433yxmyd2j8nl8qn1hw8wv3mk270dp8xxlk613y3p")))) + "1jxp4qacclfl07ig8dfwy5gpnsqrfqnjbci1a7znc7acqg0kv0zv")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -5946,14 +6399,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1h065fhw0n2ga74csyhqbj4qfhkg058pqa684ixcski4rhsd7hcf")))) + "0bgv8a7hf8ns472zfryf255zqdikjv08np6k6hkpvyivad25vpwy")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -5964,8 +6417,8 @@ problems in CEL-level data to help evaluate performance of quality metrics.") r-dbi r-edger r-gcrma - r-glimma r-ggplot2 + r-glimma r-gostats r-gplots r-hwriter @@ -5988,14 +6441,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1r1c0iwix0n8r433x4bv8hvzhkablc4xkdgg2b1fk4ijhd1iwf3c")))) + "01shv7936cb5yynxkdssczl752ayv2rx4qkrkddqhi5smksw13z9")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -6012,14 +6465,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0n86my3bzy3g7xn60kizs5ym5m016zrkg7dv96kx246mrnv0ax8y")))) + "18qjdsgkmdhwv2c4sbixp7fn69sbjdipn363jnms95dksdj2xvr9")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -6040,14 +6493,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "1104r6jdy3nza8329xmq428ljfbfi2xwkd92sw519g0yqryh09vy")))) + "10mdlbgbvdj967bih6wpvxmy91r10p8frhgcwv8mhv4g94ardasd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -6067,13 +6520,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.62.2") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0vprm84k79pfnkkg9vf3gyb1nhzmin5lp5375rsaj6fnzbd46dw9")))) + "1bdr303a2z03c8vc8q95a4a4a8i956vimia5yik78yddd1ig9gq3")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6097,13 +6550,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "10jkxjmsshrr08c397qvkgrcfwzvrbd2hci1nal4vd5mm77f9cl9")))) + "0cd2vcnx0pn5wba3x5q32vddjjp7fvix7yd7jrwv07a2fkv9c4p5")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -6122,14 +6575,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.42.2") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0b4dmjv7y50c1rn76wlhnlz93kidvg1byj72vq2s11kdzyq3pmss")))) + "0dbbg0wvk1ndv20d5j80waaz0z1bsp7y2k2m17jly4ax2hc5frc9")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6154,14 +6607,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.8.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0ri8qj5j10bhprkb810c2hl5sl944kpb8rf5lab6nxykzgyz73v0")))) + "1mx3vip1rx5lq0vnkxpmkyksnq4vygmww85vxq3spr0fah1pwnkr")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -6195,14 +6648,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "118yqvbj4ad2b2bik0zi3ir15kxh9fbdi9qqyk52isvcdbv6069p")))) + "1i6rml0slfsf01a3sphyzrxp2z759psq5bv9cfy5dxx44fnav8b8")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -6219,14 +6672,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk")))) + "1qv2gydn8awrkbhdrgxm8zxpicphqc29rwzkj3vyaa9glmnx2y34")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -6249,13 +6702,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1xjs5nxr3dffllp599hf0cx71a2czqmhf7zj2sp6rz06kcxib905")))) + "0znkawzr3hgbp2dkdk30ziqa6ylbq2nf0xmz4vi089cw9763lxgg")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -6272,13 +6725,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.56.1") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0jqv2mv4ridi5lffva20a5s479bzpxhblyymricb17fd400rag8f")))) + "1m6c6m9z0d1k6s2q0ikd78ahcq72gzqnhlprdn0xvkjxrgh1i2lf")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -6312,13 +6765,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biomartr (package (name "r-biomartr") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) (uri (cran-uri "biomartr" version)) (sha256 (base32 - "06wd8s2cssw58xp9d078fc7iycpxryccnclrk3gnh757j1h0vzim")))) + "0ic6qbk2xmgrcc0xhxyhjafp1xbf2c5dpbqqrbkprrhynr8mq7cx")))) (properties `((upstream-name . "biomartr"))) (build-system r-build-system) (propagated-inputs @@ -6357,13 +6810,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.34.2") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0j0yi0g0zri0liy9xm2j3k848smhib5mmkvwcw6281iwnpn7yypq")))) + "19h80qf0zdxfg3pkcwwywh9gg0ymv92n51qpimnw4c3w5iaszy6b")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -6408,13 +6861,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.68.1") + (version "2.70.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "13cnjbq2iykv83ycb4151d7yys21s3v15fc72v3s02m1i92lqyq4")))) + "198y36yfkncsp4sw00ij8cal45al67f9nx84bbszhygaq0jh504y")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6425,6 +6878,7 @@ objects.") r-iranges r-s4vectors r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -6436,14 +6890,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0na37f2nfavgxd2xhprfb6bv68zm2h6glbkffspc3gsnw1q5h6da")))) + "01hli49aq1fjjgpk465znq1ki0qi7nxg71pqg18fz6nblg3ny9z5")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -6478,18 +6932,19 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.68.0") + (version "1.70.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0fx2mkzyhbn8iayw14nr913wd4xhp76b1zjb85akrxaab2dm4zz8")))) + "1bdrh1kp7ihnlyvgdvwdzly69l9zy5rr09gizm0l59zy4kh59nih")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics + r-biocio r-biostrings r-genomeinfodb r-genomicranges @@ -6509,14 +6964,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1wjf6xbnys7nv8z4xrzck1wk5xifkdni672kigs0aqdxqj8d80f5")))) + "19qyxqky1gsrjylmc2h0sndbqlk2ibrps7123gqwn19p8kg4nhf0")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6524,12 +6979,12 @@ genome data packages and support for efficient SNP representation.") r-annotationdbi r-biobase r-biocgenerics + r-dbi r-genefilter r-graph r-gseabase r-matrix - r-rbgl - r-dbi)) + r-rbgl)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -6540,13 +6995,13 @@ analysis.") (define-public r-champ (package (name "r-champ") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMP" version)) (sha256 (base32 - "1px2pm90lxwh0yn7h1kmmf94flhjs5p4i0iav7ya1xfybyg4w2zc")))) + "1gdcdx34bxffd6ch354qx7yjngx3lj9chv5frwjyk56jq12vjjk7")))) (properties `((upstream-name . "ChAMP"))) (build-system r-build-system) (propagated-inputs @@ -6602,13 +7057,13 @@ regions and to highlight copy number alterations.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0nngygci1g8bb3rsica348zi59hskr6hf8319csia6cman89gvqm")))) + "0bx85y5888w85miif73y0yd9j4kdmjn1cfck1xshnqnsrh7p3m50")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -6617,18 +7072,17 @@ regions and to highlight copy number alterations.") r-aplot r-biocgenerics r-boot + r-dplyr r-enrichplot - r-iranges r-genomeinfodb - r-genomicranges r-genomicfeatures + r-genomicranges r-ggplot2 r-gplots r-gtools - r-dplyr - r-plotrix - r-dplyr + r-iranges r-magrittr + r-plotrix r-rtracklayer r-s4vectors r-tibble @@ -6650,14 +7104,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "0q83c4dm9qbdxlh4cbdzp357fn4sa16d7dqb4s65650pcnjg3a48")))) + "1fw99xnll4jwdmp49jh59zxcbp3qs2850pjdg403sv4cg1bgfdyi")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -6677,14 +7131,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "08jpbw7qns736zq1fwk9lyr4qm7rgzzw3hksv59zwb1458a79pzy")))) + "0zzp0kci5daffpyv56advdcs05pz3nmjn07bmm7r3hwpk0nr3fcf")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -6839,14 +7293,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.40.2") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0rb6b2aqn3an5ria4yjasjr7aldr5606rkc4yw275x9ddii22djg")))) + "1mz7v0vcl741zjvj63mk48hhbq6sk2fl2dwn9y1a6hr8fb79vy1a")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6857,6 +7311,7 @@ distribution.") r-ggplot2 r-iranges r-locfit + r-matrixgenerics r-matrixstats r-rcpp r-rcpparmadillo @@ -6876,14 +7331,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0z4i3lsaziq3hprk64akx7jl6b757kmd8k6gv5pn36pavc6x1a0g")))) + "1q59agaidf0nkq599iz54a253sjxzillj39za86ihfj5xws24f8w")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6921,13 +7376,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1vsn9z06vmfw6741x7dri3d9wh4rqhzak9r506y3c3h2gjjwilv1")))) + (base32 "1k3gzzgda29m2v7v8hqw7c2s8z778p0plqxag443lhsxcm6izcxi")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -6959,14 +7414,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1vslg6hp498ar4l1b8rdxscz5wj1xci866j8975wr378lnymb942")))) + "1rvic3acrf4qdag423f8xa6bnqrqr31vj7k4l7a5kzf1fjm359wy")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -6986,13 +7441,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0gpgmy1yqgxvxiyrinxnn78w68w81ldqyhzwz3yxj2brlld6ycd1")))) + "17ks6bbhv8iw8grzlkibgqmwggrqp5hikg1p49m4a6b6bayillv2")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -7030,14 +7485,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0gf4k02b5qywrg5rpg6hs9gyzcdlpw36ndgz3ca19plicair4mih")))) + "0xvi5mynkf1n74bn2k6gxmyhp1piwzsljd37biibdfzy14r1ir08")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -7070,17 +7525,18 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.42.4") + (version "4.0.9") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1lyn017jqgn6d987zrk0kp2p2nw3mxf8zjspk31pky532p9pkhs3")))) + "1jdpvswcnspiypk9c2wq01cgcv1l5061q9h8gc5khhk9jlyv44bg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -7095,13 +7551,13 @@ CAGE.") (define-public r-enhancedvolcano (package (name "r-enhancedvolcano") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnhancedVolcano" version)) (sha256 (base32 - "1mcyhgdvfmkkh0rlhf51an7j1zi96lqdhifki2aqmlx0lqvg4qxq")))) + "097w3957m47m03iy8xc1m7pdgm3qy0kzqbllic8pd79qglrla802")))) (properties `((upstream-name . "EnhancedVolcano"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrepel)) @@ -7123,13 +7579,13 @@ parameter configurations.") (define-public r-enmix (package (name "r-enmix") - (version "1.36.0") + (version "1.38.01") (source (origin (method url-fetch) (uri (bioconductor-uri "ENmix" version)) (sha256 (base32 - "1cwj45rnb6ra1bnd0plkjfvfsix25xr51yh6rwrfj524c35r70w1")))) + "1wh9lri9dp3904c2n6562z7p9gqx39dmag55imx8zrqnayxamc03")))) (properties `((upstream-name . "ENmix"))) (build-system r-build-system) (propagated-inputs @@ -7146,9 +7602,9 @@ parameter configurations.") r-illuminaio r-impute r-iranges + r-irlba r-matrixstats r-minfi - r-preprocesscore r-quadprog r-rpmm r-s4vectors @@ -7165,14 +7621,14 @@ visualization of Illumina DNA methylation array data.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1x73lln0rlnypl8iia54srl3wrazs94f8rspmjsaqsxwknkym319")))) + "010fp03x1splddxmhpxlfv1i3paqgbcxm7l9z2lmm6zfixhb158a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7207,21 +7663,53 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) +(define-public r-epidish + (package + (name "r-epidish") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EpiDISH" version)) + (sha256 + (base32 "170ym3y6gd1kxghz2g5ynvgi1wrxx87b568cjcvzidpqkrkg87s6")))) + (properties `((upstream-name . "EpiDISH"))) + (build-system r-build-system) + (propagated-inputs (list r-e1071 + r-locfdr + r-mass + r-matrix + r-matrixstats + r-quadprog + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sjczheng/EpiDISH") + (synopsis "Epigenetic dissection of intra-sample-heterogeneity") + (description + "@code{EpiDISH} is a R package to infer the proportions of a priori known +cell-types present in a sample representing a mixture of such cell-types. +Right now, the package can be used on DNAm data of whole blood, generic +epithelial tissue and breast tissue. Besides, the package provides a function +that allows the identification of differentially methylated cell-types and +their directionality of change in Epigenome-Wide Association Studies.") + (license license:gpl2))) + (define-public r-fastseg (package (name "r-fastseg") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "0gygyf1xq1z6vzand43n965p366zh0k3rv58gnyqa81whj4dvcq3")))) + "10g9mdh7nzdz2b1k5gg5hk35lpapcnbs3p3z17k15aq040lpm236")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description @@ -7237,14 +7725,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "16wx2w70i12420022xz2zx8pizzyxb7z1pcmqn515cs89f1qcnli")))) + "0bm5hvy3cdcm46527w45mnnnk95qm28xzdk1m53615gh55ix4iy8")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -7265,14 +7753,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.82.1") + (version "1.84.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1wpg8banz6s6smycfqf9hqryp4kf2gs069s7npyvpq53wy0kxyny")))) + "0q80z872d3z1jy69b53qxzvmshf5zx4qssmp4gj7fwdpfxj9qqjw")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -7289,16 +7777,16 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "1bimsayaf68j15im591r6rbvydhbmiqcp1pphd5zzg6hzp6va927")))) + "074d3inz8sh8xxjliisa0p99rgy6r9fg9ljaka5bf1waxwpknzpw")))) (build-system r-build-system) (propagated-inputs - (list r-rcolorbrewer r-gplots)) + (list r-gplots r-rcolorbrewer)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -7308,13 +7796,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0y6a2qxxp5mnkllcq46j00069z22ixnrbkd15s007a35lhkibz21")))) + "1vbpx187m5d5g307f4jiwyy1sw4jgj1s18622y3a458ixv540zkc")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -7355,13 +7843,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.4") + (version "1.38.5") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0wwh72sj894m3awk4g2zmkkwqafdjyxzsr49vnd1fiyz909hw02a")))) + "17w5zrvpk2x0sc55xfkbn9krphg4aszmvwmj1qfsf1bdrazfpwic")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7381,13 +7869,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.36.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1irzcz9s97gqbyj9j71wxv2ikdfd8g14296fg33w2ykfdm80nzf0")))) + "0i4n735xabdhlg7w2yd31lg65s9b6w12fhzij91hbcp0hs40fvw1")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7414,13 +7902,13 @@ alignments.") (define-public r-genomicdatacommons (package (name "r-genomicdatacommons") - (version "1.24.3") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicDataCommons" version)) (sha256 (base32 - "1grvria7lx7p0py3w8yi0j41bpfx951lds5db7jdiq0j8l75fh38")))) + "1inikcczkhav6h6a46ix9ixkf7b1n8rf766m5hmhmx09sspzsm5w")))) (properties `((upstream-name . "GenomicDataCommons"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -7446,13 +7934,13 @@ Commons RESTful service.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.52.2") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0givyx77gvx24wgq180jsb2q1b8g4j49rs6bxdmd0l04a87hm9cr")))) + "1b2rx16l7zd4lisqssbkcwi534s7m7h1w6k72km6c835x2cdxfs4")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7490,14 +7978,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0nxz8lvpmyllgs1ksgbha8qqs4fhppkg5casppnas9x47dj4bxph")))) + "1kvys60hhb0ndjvjdanfgciq3jc42iag8r0a199gv6w5bjaxp6wm")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -7525,13 +8013,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.52.0") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0vbr8nqn4pk0w3wx94q4f44psy6lxgx4b7p8hp0vf46flwggj2lj")))) + "1vrs3r8dyhhwj0s3vwvr168s84x5hj10lnpg1xf5c2kbj26bdv0w")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7552,13 +8040,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-glad (package (name "r-glad") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GLAD" version)) (sha256 (base32 - "0fi7wwn0ai4bwy8wgwl4dh3fbl6zhrkcy662dc1fcnk5i7rnv3y5")))) + "04wyzn56crz7sa453qj07p90vvg8nwrqz54m9ms9vf9z8adpck51")))) (properties `((upstream-name . "GLAD"))) (build-system r-build-system) (inputs (list gsl)) @@ -7576,13 +8064,13 @@ regions identified.") (define-public r-globalancova (package (name "r-globalancova") - (version "4.18.0") + (version "4.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GlobalAncova" version)) (sha256 (base32 - "1fld18rmi6rqm2nr549a4740w1iq3mf5df67v9ba6h42r4abs1ar")))) + "0j1ma04zjsvf668idms8hx1vnw3sh5yy8fbhwscyk1qbfy708cfh")))) (properties `((upstream-name . "GlobalAncova"))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -7608,13 +8096,13 @@ linear models via the extra sum of squares principle.") (define-public r-globaltest (package (name "r-globaltest") - (version "5.54.0") + (version "5.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "globaltest" version)) (sha256 (base32 - "0jjhhg4vi44xqlvmcd80m30m93qyd4c79i7m9jn5hz3mw211xaig")))) + "14kcsx1gynl0fijq67qb5zvfxn4yqj8809p7535y455rd0vddp5r")))) (properties `((upstream-name . "globaltest"))) (build-system r-build-system) (propagated-inputs @@ -7632,14 +8120,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") (define-public r-gostats (package (name "r-gostats") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1jjcjc1zp42l3gw36rr84al07ghih0cjx4p8gn8rlmv1jsz6kp1h")))) + "1v10ss1gf4a3qp6hbwa2f0la9sgiwhszg4c45qd6gv0dja2v30fs")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -7650,8 +8138,8 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") r-category r-go-db r-graph - r-rgraphviz - r-rbgl)) + r-rbgl + r-rgraphviz)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") @@ -7664,14 +8152,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0xfcgvsglcwkwsb1azmp4n4hx95fxnjk7rlwggb1f5rjw440qjnh")))) + "1y7z3627shskwss8bzjz1xm02rv4s7cdi91v1xqdsbdayjkrh1nb")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7693,13 +8181,13 @@ Enrichment Analysis} (GSEA).") (define-public r-gsva (package (name "r-gsva") - (version "1.48.3") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSVA" version)) (sha256 (base32 - "0ljfw65ray9ks8g55bfzn0c1w4412y4a7996zddywn5qj5pkjkfb")))) + "01w5j7fmi3hsfd282kcn4v41mi58z2yfhapff2zgf9swdfps4m6z")))) (properties `((upstream-name . "GSVA"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -7733,13 +8221,13 @@ manner.") (define-public r-harshlight (package (name "r-harshlight") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Harshlight" version)) (sha256 (base32 - "1rg3gx42a68jqbdmbqx7lh97y0rird1lci7146hnxa4svj827d5p")))) + "1djs95l04b3qrqcb7jkzhfmxzbsn2riyydz8p2lmilg6z9rkdqx7")))) (properties `((upstream-name . "Harshlight"))) (build-system r-build-system) (propagated-inputs @@ -7760,14 +8248,14 @@ matrix to solve the memory problem.") (define-public r-hpar (package (name "r-hpar") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1sg0mjada72a13xh3k6xsiaff7xj4mp76r6i8iab8nfkvng07p4i")))) + "19jdy0q3larl5lxjzqlnyynq9rya56fyvf1yx9pwsyag1c148z08")))) (build-system r-build-system) (arguments (list @@ -7795,13 +8283,13 @@ the Human Protein Atlas project.") (define-public r-r3cseq (package (name "r-r3cseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "r3Cseq" version)) (sha256 - (base32 "1wpjsiy9qh45h3k5s79w4zhkma5h4gvyf2sa8l934mx0jl16k0q2")))) + (base32 "1llkfcy13h0c973703jmpgp2n6xxfsizb9iw1wxzgkbp1v0iy268")))) (properties `((upstream-name . "r3Cseq"))) (build-system r-build-system) (propagated-inputs @@ -7827,13 +8315,13 @@ interactions from 3C-seq assay.") (define-public r-r4rna (package (name "r-r4rna") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "R4RNA" version)) (sha256 - (base32 "1i4c9477xsp3hq5kxydrimhl6g8vshwbqgnhap5n1ykxbsval1pp")))) + (base32 "1qmr1s7z2f126wkwxjpr9fvak4i7mzgvfflkycgavbdqshn1rk6l")))) (properties `((upstream-name . "R4RNA"))) (build-system r-build-system) (propagated-inputs (list r-biostrings)) @@ -7850,13 +8338,13 @@ with numerical methods for computing statistics for each.") (define-public r-radiogx (package (name "r-radiogx") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RadioGx" version)) (sha256 - (base32 "18zqfnwjil4mv7fgh4wvnniyybmyqkg0hk2wc57rcn0mlppa3602")))) + (base32 "0ykmvva5h1y7x9bxhqqfc18car9nasy06v1jjban7dlm95dl8nmk")))) (properties `((upstream-name . "RadioGx"))) (build-system r-build-system) (propagated-inputs @@ -7895,16 +8383,17 @@ fraction} are included.") (define-public r-raggedexperiment (package (name "r-raggedexperiment") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RaggedExperiment" version)) (sha256 (base32 - "0aa886mmk1c5h1i3xnk4niq4ylrawpsn2f62hwmfj5dsyl8a36ka")))) + "07wx2icvxgrds1w7cx9pn99z6rzk2ih938j8g1laxmgx9sya74v6")))) (properties `((upstream-name . "RaggedExperiment"))) (build-system r-build-system) - (propagated-inputs (list r-biocgenerics + (propagated-inputs (list r-biocbaseutils + r-biocgenerics r-genomeinfodb r-genomicranges r-iranges @@ -7928,13 +8417,13 @@ rectangular dataset.") (define-public r-rdisop (package (name "r-rdisop") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rdisop" version)) (sha256 (base32 - "02mj02sa9qxc6678irx7g3yzab4sa5sf4jkdjzsi9i6519xd7sa4")))) + "1jz063hsrrbrqqx8p5yknagw19hsw51arck591h95dckncxd0006")))) (properties `((upstream-name . "Rdisop"))) (build-system r-build-system) (propagated-inputs (list r-rcpp)) @@ -7950,14 +8439,14 @@ be calculated to search in MS peak lists.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1p8imns26knh21r254n7i9xvy8xzz3zizx0kq4si7cdaf2b4xayi")))) + "1h0hzs4f4mmnpi436dgib9lakljacznkyyssy7c4mdd419431aq2")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -7976,16 +8465,52 @@ nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+))) +(define-public r-rnbeads + (package + (name "r-rnbeads") + (version "2.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RnBeads" version)) + (sha256 + (base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp")))) + (properties `((upstream-name . "RnBeads"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-cluster + r-ff + r-fields + r-genomicranges + r-ggplot2 + r-gplots + r-gridextra + r-illuminaio + r-iranges + r-limma + r-mass + r-matrixstats + r-methylumi + r-plyr + r-s4vectors)) + (home-page "https://bioconductor.org/packages/RnBeads") + (synopsis "RnBeads") + (description + "@code{RnBeads} facilitates comprehensive analysis of various types of DNA +methylation data at the genome scale.") + (license license:gpl3))) + (define-public r-impute (package (name "r-impute") - (version "1.74.1") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0nz8ggzk2g5w20yyhp6av6hy69kbmg3ncfpq9ppmq6p5a0msx92l")))) + "0q7mnx99ndna1r2r0v7jc3w8ly8qw33flwbgkcvrfhk6dzvbn4pl")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -7999,52 +8524,60 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplay (package (name "r-interactivedisplay") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplay" version)) (sha256 (base32 - "1y9fdnpz1bagrwhyj8jikp2q5fd9y74j48l5z7f0s88v88sa7szl")) + "0w81c5kc48gjavln50ysgr3vaf8s4fb6632ckzb1q225j9ik2gia")) (snippet '(for-each delete-file - '("inst/www/js/jquery.js" + '("inst/www/js/d3.v2.js" + "inst/www/js/jquery.js" "inst/www/js/jquery.min.js" - "inst/www/js/jquery.dataTables.min.js"))))) + "inst/www/js/jquery.dataTables.min.js" + "inst/www/js/jquery.dataTables.nightly.js"))))) (properties `((upstream-name . "interactiveDisplay"))) (build-system r-build-system) (arguments (list - #:modules '((guix build utils) - (guix build r-build-system) - (srfi srfi-1)) + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'process-javascript - (lambda* (#:key inputs #:allow-other-keys) - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "js-jquery-1.8.2") - "inst/www/js/jquery.js") - (,(assoc-ref inputs "js-jquery-1.9.1") - "inst/www/js/jquery.min.js") - (,(search-input-file inputs - "/share/javascript/jquery.dataTables.min.js") - "inst/www/js/jquery.dataTables.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets)))))))) + #~(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/" + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "js-jquery-1.8.2") + . "www/js/jquery.js") + (,(assoc-ref inputs "js-jquery-1.9.1") + . "www/js/jquery.min.js") + (,(search-input-file inputs + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.min.js") + (,(string-append (assoc-ref inputs "js-datatables-1.9") + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.min.js") + (,(string-append (assoc-ref inputs "js-datatables-1.10") + "/share/javascript/jquery.dataTables.min.js") + . "www/js/jquery.dataTables.nightly.js") + (,(assoc-ref inputs "js-d3-v2") + . "www/js/d3.v2.js"))))))))) (propagated-inputs (list r-annotationdbi r-biocgenerics - r-biocmanager + r-biocmanager ;this is not listed in DESCRIPTION r-category - r-dt r-ggplot2 r-gridsvg r-interactivedisplaybase @@ -8052,12 +8585,19 @@ microarray data, using nearest neighbor averaging.") r-rcolorbrewer r-reshape2 r-shiny - r-zlibbioc r-xml)) (native-inputs `(("esbuild" ,esbuild) ("r-knitr" ,r-knitr) - ("js-datatables" ,js-datatables) + ("js-d3-v2" + ,(origin + (method url-fetch) + (uri "https://web.archive.org/web/20230428092426id_/https://d3js.org/d3.v2.js") + (sha256 + (base32 + "1m57mxhcynfaz6gz3v0aph5i6hx5jf455jdygyl8yzs9r2dpp5vr")))) + ("js-datatables-1.9" ,js-datatables-1.9) + ("js-datatables-1.10" ,js-datatables) ("js-jquery-1.8.2" ,(origin (method url-fetch) @@ -8083,14 +8623,14 @@ visualizations and interfaces for working with Bioconductor data.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1p3lwk8g14srkhl3x3i0v2d9071251ldy9964mii11k1bp2g08am")))) + "14cw90qlp8y4k0fs7xim8qvhzwbb8sn334mc72fkxg1h4bs8bxjw")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -8108,14 +8648,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "13pbw5nlkjwplliv2pdwazv2idfjklvw0ykx5ja8rchvzs5f1vk4")))) + "05fc1i1bcdvvy4mr4m2cdqxd3jrj1rxkxy7c43yrliv5dlikyb07")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -8132,13 +8672,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lea (package (name "r-lea") - (version "3.12.2") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "LEA" version)) (sha256 (base32 - "1kxrrl8pxhaipmzsw8gs4gs8g8xbp8169z9f7bcpgrfapnawafm9")))) + "1rhlrcp9rzf64rkabgk3gd8jqdg8ldwpkxvpfb6g49bgpkg1h6b1")))) (properties `((upstream-name . "LEA"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8163,13 +8703,13 @@ scale with the dimensions of large data sets.") (define-public r-lfa (package (name "r-lfa") - (version "2.0.11") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "0x169fxwlccsqwj1bpviaky3hfr0zdwsdrlgfvrb4j6j95qfgnns")))) + (base32 "1xrwvw7227znd1h7426k8l86197yc24b4v608issh5fqglmhljns")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor r-rspectra)) @@ -8184,14 +8724,16 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.56.2") + (version "3.58.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0miyba9frn1p4pkclzpr0bfazsk0br2jgpwpwwh773d3103hkn0r")))) + "01byjnhhjyxk9x871rk8bgqq6lkp1a6dylqbdphpzp88b1jf2f9m")))) (build-system r-build-system) + (native-inputs (list r-knitr)) + (propagated-inputs (list r-statmod)) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") (description "This package can be used for the analysis of gene expression @@ -8203,13 +8745,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-maaslin2 (package (name "r-maaslin2") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Maaslin2" version)) (sha256 - (base32 "06mb72hbzihdficv73yqbb2m86bkw78w3vbw1rm98n0npxq2fch6")))) + (base32 "1d95dv46b36ncwb7zdn0wvshg4v73qjfs3hij0jmbkkxvf2il9iq")))) (properties `((upstream-name . "Maaslin2"))) (build-system r-build-system) (propagated-inputs @@ -8251,13 +8793,13 @@ of data exploration, normalization, and transformation methods.") (define-public r-made4 (package (name "r-made4") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "1233l5160msxp85vm2h0j3k073vv5d9wj55709x4s657fi9la6ij")))) + "03fhiszlmjh8nvz3gppf45r9kpcjrdb601ar17c4f2aygjpkf0cg")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -8280,13 +8822,13 @@ datasets (coinertia analysis).") (define-public r-makecdfenv (package (name "r-makecdfenv") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "makecdfenv" version)) (sha256 (base32 - "1a6kngwmc7nvzlgpnhdv4j180847gjh4i3dshld0pcvy3b6bjv8r")))) + "0mggcw0390i1y2wn4k8570gjmbsx6hbipi8fkhz2zj9icsx89x1l")))) (properties `((upstream-name . "makecdfenv"))) (build-system r-build-system) (inputs (list zlib)) @@ -8307,13 +8849,13 @@ package that automatically loads that environment.") (define-public r-manor (package (name "r-manor") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MANOR" version)) (sha256 - (base32 "0ili9xy7vvw17mz44lxadv1vkf3ahpks2l34qa9yfccpalwhzriw")))) + (base32 "10zf6c1vx6cp4wg6axpmbpxk2hlmf6mga7rdh765fznwb71r4h0x")))) (properties `((upstream-name . "MANOR"))) (build-system r-build-system) (propagated-inputs (list r-glad)) @@ -8330,13 +8872,13 @@ experiments.") (define-public r-maser (package (name "r-maser") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maser" version)) (sha256 (base32 - "1ma5d1i56gw8hm2pgvzzvmdd1cm2xb42rgf5lb6sf4v47yzlyb9f")))) + "0h7x1fyfvnjc30w9ydbnlqijz58q2kcxv4yy784rf4adsrdhwh45")))) (properties `((upstream-name . "maser"))) (build-system r-build-system) (propagated-inputs @@ -8362,13 +8904,13 @@ and visualizaton of alternative splicing events generated by rMATS.") (define-public r-mdqc (package (name "r-mdqc") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mdqc" version)) (sha256 - (base32 "0y35z9sw3h77a5g4ah0fxrk5xh7irdw9z0y2jhh6dp0xxcqh6i0k")))) + (base32 "0q6ig9qdf2s9329wysrvgh13yq5c7n76as2c3mahqm78xb0mpplf")))) (properties `((upstream-name . "mdqc"))) (build-system r-build-system) (propagated-inputs @@ -8384,16 +8926,42 @@ array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.") (license license:lgpl2.0+))) +(define-public r-metabocoreutils + (package + (name "r-metabocoreutils") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MetaboCoreUtils" version)) + (sha256 + (base32 "0bs24dwqlm8isp231jds51l7v16q0gjli1qmhjxyva3qmi5yb4dl")))) + (properties `((upstream-name . "MetaboCoreUtils"))) + (build-system r-build-system) + (propagated-inputs (list r-mscoreutils)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/MetaboCoreUtils") + (synopsis "Core utils for Metabolomics data") + (description + "@code{MetaboCoreUtils} defines metabolomics-related core functionality +provided as low-level functions to allow a data structure-independent usage +across various R packages. This includes functions to calculate between +ion (adduct) and compound mass-to-charge ratios and masses or functions to +work with chemical formulas. The package provides also a set of adduct +definitions and information on some commercially available internal standard +mixes commonly used in MS experiments.") + (license license:artistic2.0))) + (define-public r-metagenomeseq (package (name "r-metagenomeseq") - (version "1.42.0") + (version "1.43.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metagenomeSeq" version)) (sha256 - (base32 "0293c531l0sjz8qxy7nrajfl081v9df0af9242017msbvyszq6wk")))) + (base32 "1m19qkwrbfr4yhbr1izfjka3brn1qasqql6alczv55l5h52m4s4b")))) (properties `((upstream-name . "metagenomeSeq"))) (build-system r-build-system) (propagated-inputs @@ -8421,13 +8989,13 @@ correlations.") (define-public r-metaneighbor (package (name "r-metaneighbor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 - "151ip70la12kj80c0airi1yyjbj69gnkshd6kfk88wsvq7s179id")))) + "0y8nk9jq0z48phg13mf6hsfg8l54w6z6b67g0k1c9gmsb7aqq04d")))) (properties `((upstream-name . "MetaNeighbor"))) (build-system r-build-system) (propagated-inputs @@ -8454,16 +9022,54 @@ on the basis that cells of the same type should have more similar gene expressio profiles than cells of different types.") (license license:expat))) +(define-public r-methylaid + (package + (name "r-methylaid") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MethylAid" version)) + (sha256 + (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d")))) + (properties `((upstream-name . "MethylAid"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-ggplot2 + r-gridbase + r-hexbin + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://git.bioconductor.org/packages/MethylAid") + (synopsis + "Quality control of large Illumina DNA Methylation array data sets") + (description + "This package provides a visual and interactive web application using +RStudio's shiny package. Bad quality samples are detected using sample-dependent +and sample-independent controls present on the array and user adjustable +thresholds. In depth exploration of bad quality samples can be performed using +several interactive diagnostic plots of the quality control probes present on +the array. Furthermore, the impact of any batch effect provided by the user can +be explored.") + (license license:gpl2+))) + (define-public r-methylkit (package (name "r-methylkit") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1qi4gwlxsxr4cgs8s12qybrs89vr79xwd7n9in1af3hyn0swikn1")))) + "0y45wa45kblm2g3nylvybvyfc34sjlynhsz3dirhs1favb83sdiv")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -8504,13 +9110,13 @@ TAB-Seq.") (define-public r-mfuzz (package (name "r-mfuzz") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Mfuzz" version)) (sha256 (base32 - "0rfna5ycwkx4xb2gv1wpfn7f7nz6f79w5nlkb7719l5730d81wnz")))) + "0v2l3fi9331lxfam6az265rfk52g4n75hh4rg12ykhp86ihplzpf")))) (properties `((upstream-name . "Mfuzz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) @@ -8524,13 +9130,13 @@ time-series data (including a graphical user interface).") (define-public r-mmuphin (package (name "r-mmuphin") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 - (base32 "14cn1mg9ffhzy1vgschl2h0wzah3c1g67q367f2m050a3z2i2ndy")) + (base32 "0lhvsx5yjvqh5d3h860sv8cf3h73nrzvljpkqrd9ks0irc4gcm6d")) ;; Delete generated files. (snippet '(for-each delete-file @@ -8589,6 +9195,43 @@ It has function interfaces for: @end itemize") (license license:expat))) +(define-public r-modstrings + (package + (name "r-modstrings") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Modstrings" version)) + (sha256 + (base32 "1jjawwkvdx02ss2vw4ah2b8psgxr01z6r1rkr2pnkmrp2ma7ygks")))) + (properties `((upstream-name . "Modstrings"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/Modstrings") + (synopsis "Working with modified nucleotide sequences") + (description + "Representing nucleotide modifications in a nucleotide sequence is +usually done via special characters from a number of sources. This represents +a challenge to work with in R and the Biostrings package. The Modstrings +package implements this functionallity for RNA and DNA sequences containing +modified nucleotides by translating the character internally in order to work +with the infrastructure of the Biostrings package. For this the +@code{ModRNAString} and @code{ModDNAString} classes and derivates and +functions to construct and modify these objects despite the encoding issues +are implemenented. In addition the conversion from sequences to list like +location information (and the reverse operation) is implemented as well.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") @@ -8619,14 +9262,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1jcy07m8ywpgsmwkq6s7zj32w7gvxqj52j562irv2h2q429awdxk")))) + "0vasr9rwnfjxbb3y2saq7gqzis5xyamgvns2rlywdxv1jm0nr8y3")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -8669,14 +9312,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h")))) + "19ya4ax6pa727hdn0118l9pwa9dxgh89dz54mm66dawxga3jhar4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -8715,13 +9358,13 @@ in SNV base substitution data.") (define-public r-msa (package (name "r-msa") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 - "08fg4y8rmkvilsx2hxqwxa90p2wqrl4iyndp7wfjicvplmaxp708")))) + "1csa8j64xrfr6kdnndr3876bplclca9wf6ydy9kg97xsjq7gz8q5")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs @@ -8746,14 +9389,14 @@ package TeXshade.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.26.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g")))) + "1622mmm5n8yl4qjq8bda7689qdfz1rhyxyh8s3q5475al1d0mpsl")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -8791,14 +9434,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc")))) + "1hmfh7v7p5d741x2wh1njqwkmfmf3xmwkqy88kalrcjzrdwfpv9b")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -8819,8 +9462,8 @@ of mass spectrometry based proteomics data.") r-foreach r-ggplot2 r-iterators - r-msnbase r-msmstests + r-msnbase r-mzid r-mzr r-protgenerics @@ -8848,14 +9491,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0grl7798vnpxb6nw98zj0lbvsrhkjfsyn0y15bi4v7vhyhkk26xm")))) + "1rgkd9iv0lxj1zxh96sifwa312ivw5kl5jw82ma4fmapr4iqhzsh")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -8879,14 +9522,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.34.1") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1jsna4xwyph1gg72wwqlpavb65g5nc3db1vmcs1qcw1mdgasdjhk")) + "0z6ckp69syrdzhp6n4n399k2lar3w4n2d1ji2f90951c4ds6hkh8")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -8999,14 +9642,14 @@ Gao et al in Nature Biotechnology 2022}.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p")))) + "1s55fiqgxrdznn43qhm5yv9gp8d1msr2f39wxih0b5bm4wxhkq45")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -9038,14 +9681,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1pw3qd6n0xf7vq3x73612bndcqhwrqkpi29f6crazdzjcy3fivlb")))) + "0g75y21lqmwsh28nx99zp2gxr6rhlhbw76f66qx5hrh6bm2zpm7j")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -9071,13 +9714,13 @@ the fact that each of these packages implements a select methods.") (define-public r-oscope (package (name "r-oscope") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 - "055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v")))) + "1li2l9mdq2q0580a7qzvfid5n15v62fr9ys87j42k3l2w5a26smf")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) @@ -9097,14 +9740,14 @@ insertion module to recover the base cycle order for each oscillator group.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx")))) + "0ihc9jqjy0nl4pfgcxczfdf973nb99325agk73y0222ad1mpkc07")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -9152,14 +9795,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.92.0") + (version "1.94.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6")))) + "1asm4iafdzm98iv2j9sxvn5y9ss2p679cx7gwjipq8mf1d7bzfp0")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9179,13 +9822,13 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-pfamanalyzer (package (name "r-pfamanalyzer") - (version "1.0.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pfamAnalyzeR" version)) (sha256 (base32 - "0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy")))) + "0qxxp7kfwbb9q471mgwc4bd8dmyid56ddyzw2jlg4gb1wcq9py67")))) (properties `((upstream-name . "pfamAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) @@ -9202,13 +9845,13 @@ domain isotypes from pfam data.") (define-public r-piano (package (name "r-piano") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "piano" version)) (sha256 - (base32 "0rm9afgq4n7yinmx09b0xd17wgzhbswm80vcjmmwxr6fv1741xfy")))) + (base32 "0rw55ig3pbvi2kyg10rx60ldcncsd4gki2h1zpr1nhmqg3fv0l5y")))) (properties `((upstream-name . "piano"))) (build-system r-build-system) (propagated-inputs @@ -9236,6 +9879,65 @@ package contains functions for combining the results of multiple runs of gene set analyses.") (license license:gpl2+))) +(define-public r-polyester + (package + (name "r-polyester") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "polyester" version)) + (sha256 + (base32 "1iycdxj0jhh2faclfzflp2cjc2zmxmhy03avv75h0qg3j5kf35l4")))) + (properties `((upstream-name . "polyester"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-iranges + r-limma + r-logspline + r-s4vectors + r-zlibbioc)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/polyester") + (synopsis "Simulate RNA-seq reads") + (description + "The polyester package simulates RNA-seq reads from differential expression +experiments with replicates. The reads can then be aligned and used to perform +comparisons of methods for differential expression.") + (license license:artistic2.0))) + +(define-public r-powertcr + (package + (name "r-powertcr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "powerTCR" version)) + (sha256 + (base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i")))) + (properties `((upstream-name . "powerTCR"))) + (build-system r-build-system) + (propagated-inputs + (list r-cubature + r-doparallel + r-evmix + r-foreach + r-magrittr + r-purrr + r-truncdist + r-vegan + r-vgam)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/powerTCR") + (synopsis "Model-based comparative analysis of the TCR repertoire") + (description + "This package provides a model for the clone size distribution of the +@acronym{TCR, T-cell receptor} repertoire. Further, it permits comparative +analysis of TCR repertoire libraries based on theoretical model fits.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs @@ -9281,14 +9983,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "0fgsb47qrvrl4y3yr094mas22rai5h5yl9mciadd6zcpamp2p01i")))) + "1gjva76nxa9nzzmc9hya3bq7hswfmjd768v21f6m3gyygxvl581m")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9301,14 +10003,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0y6ghiwraw3whs57i31qnvlvqlbl9143wxv2yg48rp7qxipxvn6s")))) + "0hxhl1l6qdi355w5y7fdq8vlba2pknfizggkgr2fp8f1f3zqh494")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -9324,13 +10026,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.26.0") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "073fhbh0pzyca90q2irbaiwj21sci8jf9ksflx9pm9fr1giy37i4")))) + "19ildsck3g8v4w0g2f473sb8hyhn4avprdi78fim0prva5f9nqnv")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -9356,9 +10058,9 @@ the graph algorithms contained in the Boost library.") r-plotrix r-proxy r-ranger + r-rmarkdown r-rsqlite r-rtracklayer - r-rmarkdown r-s4vectors pandoc)) (native-inputs @@ -9371,17 +10073,54 @@ library implementing most of the pipeline's features.") (home-page "https://github.com/BIMSBbioinfo/RCAS") (license license:artistic2.0))) +(define-public r-rcy3 + (package + (name "r-rcy3") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RCy3" version)) + (sha256 + (base32 "0qkjprf2p641j3a60av1l87pd6p17za5w6bp9qyah97jmm19za7m")))) + (properties `((upstream-name . "RCy3"))) + (build-system r-build-system) + (propagated-inputs (list r-base64enc + r-base64url + r-biocgenerics + r-fs + r-glue + r-gplots + r-graph + r-httr + r-irdisplay + r-irkernel + r-rcolorbrewer + r-rcurl + r-rjsonio + r-stringi + r-uuid + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/cytoscape/RCy3") + (synopsis "Functions to access and control Cytoscape") + (description + "Vizualize, analyze and explore networks using Cytoscape via R. Anything +you can do using the graphical user interface of Cytoscape, you can now do +with a single RCy3 function.") + (license license:expat))) + (define-public r-regioner (package (name "r-regioner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0grlqga9d6mch9l487fdll65wi0m2kpq2097igfhx185i8jvwsz1")))) + "1qcgbj7d2fngs3p9a9apnj14x35kc651fy3m0651dnqrxz8j5yij")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -9405,18 +10144,16 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.39.0") + (version "2.42.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "15h7vqdxfv7y0f82ff7a8brqnscs324x22izlkgjk2wqahnmr2l1")) + "109vmrdsjdjnfrlcdyadzbwz9a50hqaahf7dawwxkbbh4mmdih78")) (snippet - '(for-each delete-file - (list "inst/doc/jslib/jquery-1.8.0.min.js" - "inst/extdata/jslib/jquery-1.8.0.min.js"))))) + '(delete-file "inst/extdata/jslib/jquery-1.8.0.min.js")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -9424,25 +10161,20 @@ region sets and other genomic features.") (list #:modules '((guix build utils) (guix build r-build-system) - (srfi srfi-1)) + (guix build minify-build-system) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) #:phases - '(modify-phases %standard-phases + '(modify-phases (@ (guix build r-build-system) %standard-phases) (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "_") - "inst/doc/jslib/jquery-1.8.0.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets))) - (copy-file "inst/doc/jslib/jquery-1.8.0.min.js" - "inst/extdata/jslib/jquery-1.8.0.min.js")))))) + (for-each (match-lambda + ((source . target) + (minify source #:target target))) + `((,(assoc-ref inputs "_") + . "inst/extdata/jslib/jquery-1.8.0.min.js")))))))) (propagated-inputs (list r-annotate r-annotationdbi @@ -9464,7 +10196,7 @@ region sets and other genomic features.") r-r-utils r-xml)) (native-inputs - (list esbuild r-knitr + (list esbuild r-rmarkdown (origin (method url-fetch) (uri "https://code.jquery.com/jquery-1.8.0.js") @@ -9488,16 +10220,16 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.44.0") + (version "2.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0")))) + "0yfy0y9ywzbbdmvvraxmizv3w2x1iznhfys6hhwyi644pxh4k3xn")))) (build-system r-build-system) (propagated-inputs - (list r-rhdf5filters r-rhdf5lib)) + (list r-rhdf5filters r-rhdf5lib r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") @@ -9515,42 +10247,26 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.12.1") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m")))) + "0cqf7k19k4m4swd2c1wd9cyzw9k90s3d3jq0hijjwvza50nn2dk6")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (arguments (list - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'use-system-libraries - (lambda _ - (substitute* "src/blosc/Makefile.in" - (("libblosc.a: blosc") "libwhatever.a:") - (("libblosc.a") - (string-append #$(this-package-input "c-blosc") - "/lib/libblosc.so")) - (("../zstd/libzstd.a") "-lzstd")) - (substitute* "src/bzip2/Makefile" - (("libH5Zbz2.so: bzip2-1.0.8/libbz2.a") "libH5Zbz2.so:") - (("./bzip2-1.0.8/libbz2.a") "-lbz2")) - (substitute* "src/zstd/Makefile" - (("libH5Zzstd.so: libzstd.a") "libH5Zzstd.so:") - (("libzstd.a") "-lzstd")) - (substitute* "src/vbz/Makefile" - (("../zstd/libzstd.a") "-lzstd"))))))) + #:configure-flags + '(list "--without-bundled-libs"))) (propagated-inputs (list r-rhdf5lib)) (inputs (list bzip2 c-blosc zlib (list zstd "lib"))) (native-inputs - (list r-biocstyle r-knitr r-rmarkdown)) + (list r-knitr)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -9561,13 +10277,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "18kh6vmyjmv7zklqr5ifpfixjwldxgwj550c69mqfkk7m0zk52cl")))) + "0bcapiwdzv7rqgs4hmw7hq290r3pz5vvhg4apxard0yybq83na1g")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -9590,7 +10306,8 @@ HDF5 datasets.") r-iranges r-rhtslib r-s4vectors - r-xvector)) + r-xvector + r-zlibbioc)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") @@ -9627,13 +10344,13 @@ tab-delimited (tabix) files.") (define-public r-rtcga (package (name "r-rtcga") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGA" version)) (sha256 (base32 - "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25")))) + "1lzdwkisvzj1wyx3wx4ll1c2j9ww3xz8kpbngmpf8cdrw4h3jrg1")))) (properties `((upstream-name . "RTCGA"))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -9672,13 +10389,13 @@ transforms TCGA data to tidy form which is convenient to use.") (define-public r-rtcgatoolbox (package (name "r-rtcgatoolbox") - (version "2.30.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGAToolbox" version)) (sha256 (base32 - "03p5rgjzc1265q60jkvk92vhcib5wdnv6bz997r70q9c39y03wm5")))) + "1a38b30nsg2bnlnijf4aa4rn4db2y4v86awfbf6a6qzqwlzknrcq")))) (properties `((upstream-name . "RTCGAToolbox"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -9688,7 +10405,6 @@ transforms TCGA data to tidy form which is convenient to use.") r-genomicranges r-httr r-raggedexperiment - r-rcircos r-rcurl r-rjsonio r-rvest @@ -9712,13 +10428,13 @@ pre-processed data.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.60.1") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8")))) + "1jxhv2fq62lz0j6kbwq43c8ggk14ccsjg0xgfqjqy941dj9ig0n2")))) (build-system r-build-system) (arguments `(#:phases @@ -9791,13 +10507,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-saturn (package (name "r-saturn") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "satuRn" version)) (sha256 (base32 - "0frm7iblxkc8ajcdqrfgsvf4krn6x8cr3mx7fnzq06xij0mqm3sj")))) + "12bivj0cnp38apwi3jqmil8bwsfa96cjp5f132a5raacd2z87gqf")))) (properties `((upstream-name . "satuRn"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -9825,13 +10541,13 @@ transcripts in groups of interest.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "0mxq2dknrhgj1487kfshkayx963c7qdgxwmlh9fbfr0lwc7gljfn")))) + (base32 "13wrxxdwphngi0f9vxakykk54bqngw8g38w6wkk96999lzb3p57p")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -9862,13 +10578,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0lvacrgfj9i8mwlcv5ykxs69hd3bm6bvr6fsddxffsr7cckpn31w")))) + (base32 "1f3n1m6fjx965wm2jllzk51ssj92ifxb4bln4vwk25qxd3g0bna8")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -9905,6 +10621,49 @@ comprehensive scDblFinder method.") (license license:gpl3))) ;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scgate + (package + (name "r-scgate") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scGate" version)) + (sha256 + (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (properties `((upstream-name . "scGate"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-patchwork + r-reshape2 + r-seurat + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/scGate") + (synopsis + "Marker-based cell type purification for single-cell sequencing data") + (description + "This package provides a method to purify a cell type or cell population +of interest from heterogeneous datasets. scGate package automatizes +marker-based purification of specific cell populations, without requiring +training data or reference gene expression profiles. scGate takes as input a +gene expression matrix stored in a Seurat object and a @acronym{GM, gating +model}, consisting of a set of marker genes that define the cell population of +interest. It evaluates the strength of signature marker expression in each +cell using the rank-based method UCell, and then performs @acronym{kNN, +k-nearest neighbor} smoothing by calculating the mean UCell score across +neighboring cells. kNN-smoothing aims at compensating for the large degree of +sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed +signature scores is applied in binary decision trees generated from the +user-provided gating model, to annotate cells as either “pure” or “impure”, +with respect to the cell population of interest.") + (license license:gpl3))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-scistreer (package (name "r-scistreer") @@ -9944,13 +10703,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.22.3") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "06i3r7zybwcgnak9ml2jaz7fy70zjqdh28v03ckaqhvck49kdqdm")))) + (base32 "1sd5ixs8fbiqqp1p4p505l1f0lncmagkhzh4xrk8wrca6db6k6d8")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -9983,16 +10742,91 @@ a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.") (license license:gpl3))) +(define-public r-screpertoire + (package + (name "r-screpertoire") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scRepertoire" version)) + (sha256 + (base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1")))) + (properties `((upstream-name . "scRepertoire"))) + (build-system r-build-system) + (propagated-inputs + (list r-doparallel + r-dplyr + r-ggalluvial + r-ggplot2 + r-ggraph + r-igraph + r-plyr + r-powertcr + r-reshape2 + r-rlang + r-seuratobject + r-singlecellexperiment + r-stringdist + r-stringr + r-summarizedexperiment + r-tidygraph + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scRepertoire") + (synopsis "Toolkit for single-cell immune receptor profiling") + (description + "The scRepertoire package was built to process data derived from the 10x +Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and +@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with +the popular Seurat and SingleCellExperiment R packages. It also allows for +general analysis of single-cell clonotype information without the use of +expression information. The package functions as a wrapper for Startrac and +powerTCR R packages.") + (license license:gpl2))) + +(define-public r-scrnaseq + (package + (name "r-scrnaseq") + (version "2.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scRNAseq" version + 'experiment)) + (sha256 + (base32 "0dbh3sqq7lkkdf7vls5qg7fbn6y74c7hsigb4d69pvk934ll88aw")))) + (properties `((upstream-name . "scRNAseq"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-biocgenerics + r-ensembldb + r-experimenthub + r-genomicfeatures + r-genomicranges + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scRNAseq") + (synopsis "Collection of public single-cell RNA-seq datasets") + (description + "This package contains gene-level counts for a collection of public +@code{scRNA-seq} datasets, provided as @code{SingleCellExperiment} objects +with cell- and gene-level metadata.") + (license license:cc0))) + (define-public r-scry (package (name "r-scry") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz")))) + "0hbdsjsn0jl0dr2ly5vx0wb4bnz7nl15kkypryywjvis9rdasjj3")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs @@ -10017,13 +10851,13 @@ single-cell RNA-seq.") (define-public r-seqarray (package (name "r-seqarray") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SeqArray" version)) (sha256 (base32 - "1771vk23psjavvi1nf2z8i2xawygdh4amawlijnskci8y9w4x5dm")))) + "0zs60yh3x6kgy6izn11d400vw59ww2w6bmhg6fw5ijinknyr3ixc")))) (properties `((upstream-name . "SeqArray"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -10047,14 +10881,14 @@ data access using the R programming language.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "0727yrmm194gskrcpmq4fh0qmi6dnp70gx627psrpvzlk6vlcl8k")))) + "106359wn4v0m53b33x4zjsyjsj4j8h7bnvd1whamsig982h6szp2")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -10070,13 +10904,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "033hss67dxi6fbvn6ya7vc61f60m20hwms9kmdia0icyp8nv2yil")))) + "0rs9dy540d4agp7fc8glbrcnly4s6qcxqsq4yv8y555bbdld6dv0")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -10093,13 +10927,13 @@ reference point and sorted by a user defined feature.") (define-public r-sesame (package (name "r-sesame") - (version "1.18.4") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sesame" version)) (sha256 (base32 - "1il33ygys6y72l8p3fhx301q16w9kylfy6w92b64n8gqkn6dmsmn")))) + "0yh4mrsj3pqhjkrq5dwmcpcqwixs0pmjy7dfa3cr0mf52fgzcvmr")))) (properties `((upstream-name . "sesame"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache @@ -10135,13 +10969,13 @@ and advanced quality control routines.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "0hq1q66vjd9pwdwm9zx8q45ws65bn6cm87zmjmyc3md8dwvb8cck")))) + "1gkj15q1rxvsdzbsp3gkk02kvvx0kq4wsqycf3ln1bszb9688jw6")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs @@ -10163,14 +10997,14 @@ methylation array data. Both the 450k and EPIC array are supported.") (define-public r-shortread (package (name "r-shortread") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0wpr3ksr7j5yk6m1zaa47dwdgznajsz8as4p9vf7schaqvhq1wc4")))) + "0fgiszb5qhplppfngpi4s33sx62ff5sdhd6n31a3b6l7fnlvk51m")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -10183,11 +11017,11 @@ methylation array data. Both the 450k and EPIC array are supported.") r-genomeinfodb r-genomicalignments r-genomicranges - r-rhtslib r-hwriter r-iranges r-lattice r-latticeextra + r-rhtslib r-rsamtools r-s4vectors r-xvector @@ -10203,17 +11037,60 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-sictools + (package + (name "r-sictools") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SICtools" version)) + (sha256 + (base32 "0bcajjvkaxmr8bdij8xln7a3nmxbm7jkjvg2v6p8kd0xr3q9a70q")))) + (properties `((upstream-name . "SICtools"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-curses + (lambda _ + (substitute* "src/Makefile" + (("^LIBCURSES.*") + "LIBCURSES=-lncurses\n"))))))) + (propagated-inputs (list r-biostrings + r-doparallel + r-genomicranges + r-iranges + r-matrixstats + r-plyr + r-rsamtools + r-stringr)) + (inputs (list ncurses)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/SICtools") + (synopsis + "Find SNV/Indel differences between two bam files with near relationship") + (description + "This package is to find SNV/Indel differences between two @file{bam} +files with near relationship in a way of pairwise comparison through each base +position across the genome region of interest. The difference is inferred by +Fisher test and euclidean distance, the input of which is the base +count (A,T,G,C) in a given position and read counts for indels that span no +less than 2bp on both sides of indel region.") + (license license:gpl2+))) + (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "1vs57j361fbwv7vaybs71vc208qn76djmbmakhwwcvxwrx77jp5f")))) + "0qhrlhf881mi2v0n0y410c0bf2cm3imrlglq8argnw86n9xj51pw")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -10247,13 +11124,13 @@ and comparing the clusterings.") (define-public r-singscore (package (name "r-singscore") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "singscore" version)) (sha256 (base32 - "1s1kyvkbfgwskf0hi4b44c2yx256rjp1yk9ijpld9qlm7z7pi67q")))) + "0hafzbhbik1512pisjvnnzmy8pl2shrgra6l06kpvsrczkqlmi04")))) (properties `((upstream-name . "singscore"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10285,13 +11162,13 @@ level.") (define-public r-tcgautils (package (name "r-tcgautils") - (version "1.20.4") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAutils" version)) (sha256 (base32 - "02mkijvh2h58wg7hsi76ycw6gapl0ai190agckaw4l54sqpsx91q")))) + "16pcz52ynx0syb5bcnkywllqxcfp7jipqgzgjr7q70k1z13ah7a3")))) (properties `((upstream-name . "TCGAutils"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -10324,13 +11201,13 @@ identifier translation via the GDC API.") (define-public r-tkwidgets (package (name "r-tkwidgets") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tkWidgets" version)) (sha256 (base32 - "1xp0gdfrhhfzfww4ig3y90f7334y24rhzrmlxmm4wav8slvcran2")))) + "11a8rflmga2d63l5nzdlbkyfnzsf20dzg2sy6qr143hg9sjzqrrj")))) (properties `((upstream-name . "tkWidgets"))) (build-system r-build-system) (propagated-inputs (list r-dyndoc r-widgettools)) @@ -10340,16 +11217,55 @@ identifier translation via the GDC API.") "This package implements widgets to provide user interfaces.") (license license:artistic2.0))) +(define-public r-toast + (package + (name "r-toast") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TOAST" version)) + (sha256 + (base32 "00wpgs2zdrgrh9xmp6m5h9xgv85mhdi36qvwg9gwbz9i7cfabmy1")))) + (properties `((upstream-name . "TOAST"))) + (build-system r-build-system) + (propagated-inputs (list r-corpcor + r-doparallel + r-epidish + r-ggally + r-ggplot2 + r-limma + r-nnls + r-quadprog + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TOAST") + (synopsis "Tools for the analysis of heterogeneous tissues") + (description + "This package is devoted to analyzing high-throughput data (e.g. gene +expression microarray, DNA methylation microarray, RNA-seq) from complex +tissues. Current functionalities include + +@enumerate +@item detect cell-type specific or cross-cell type differential signals +@item tree-based differential analysis +@item improve variable selection in reference-free deconvolution +@item partial reference-free deconvolution with prior knowledge. +@end enumerate") + (license license:gpl2))) + +;; TODO: check javascript (define-public r-trackviewer (package (name "r-trackviewer") - (version "1.36.2") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "trackViewer" version)) (sha256 (base32 - "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1")) + "008d1wg8882iq7jfmwijpchxrfva5ysl45ama62iy8s9dm0fpwsj")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "trackViewer"))) @@ -10409,13 +11325,13 @@ methylation data.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "0i38zs33drzk9szy2mdfs9ff9c3ccjgiyyynrrsinrx0szc8l22r")))) + (base32 "1lbla2syljpmgdf7da7vl1260fy54xs3hk6m2gjpark0dka0kqbh")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -10459,14 +11375,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "1q3c226fskl45gq28xj2w5paz2s9n9kxm0bkkgg0329w399cs09k")))) + "0pqdl0v16q90ffxla34rp07mq0if1q9izpbimfnq0rx7633mk95v")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -10483,16 +11399,83 @@ includes a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.") (license license:gpl3))) +(define-public r-trna + (package + (name "r-trna") + (version "1.20.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tRNA" version)) + (sha256 + (base32 + "0mcpql3zf1gw2k6gfyqycycc8li00818gd9qzs8s3wva7kxbpn89")))) + (properties + `((upstream-name . "tRNA"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-ggplot2 + r-iranges + r-modstrings + r-s4vectors + r-scales + r-stringr + r-structstrings + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tRNA") + (synopsis "Analyzing tRNA sequences and structures") + (description + "The tRNA package allows tRNA sequences and structures to be accessed and +used for subsetting. In addition, it provides visualization tools to compare +feature parameters of multiple tRNA sets and correlate them to additional +data. The tRNA package uses GRanges objects as inputs requiring only few +additional column data sets.") + (license license:gpl3))) + +(define-public r-trnadbimport + (package + (name "r-trnadbimport") + (version "1.20.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tRNAdbImport" version)) + (sha256 + (base32 "1i2mismx914ijys13wwz50gkk682rklp36aci270nc7vx78hynni")))) + (properties `((upstream-name . "tRNAdbImport"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-genomicranges + r-httr2 + r-iranges + r-modstrings + r-s4vectors + r-stringr + r-structstrings + r-trna + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tRNAdbImport") + (synopsis "Importing from tRNAdb and mitotRNAdb as GRanges objects") + (description + "@code{tRNAdbImport} imports the entries of the @code{tRNAdb} and +@code{mtRNAdb} as GRanges object.") + (license license:gpl3))) + (define-public r-scds (package (name "r-scds") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scds" version)) (sha256 (base32 - "059gahl679if8xsfgpxmi3h9fiagb6v08rd6rs7yv96s3pb8qywn")))) + "0cmzvc1m29ijhzs2p407bhhxfqbflzsnrk7nq0jshjyw6v6pkfn0")))) (properties `((upstream-name . "scds"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -10514,13 +11497,13 @@ scRNA-seq data computationally.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "1xr17rg8nfpcvdwa19qrcaqffkz048l5lkqlm6gw0abm8bg2k8x7")))) + "0q3j0jpc4mnmjb3xha5cmfhk1qdr1jiz7kdghznk4zqxn4bchc1d")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -10586,19 +11569,20 @@ tools either included in speaq or available elsewhere on CRAN.") (define-public r-spectra (package (name "r-spectra") - (version "1.10.3") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Spectra" version)) (sha256 (base32 - "1fx6xkl29frfk8bzz5jvr1cn0hjyi46ck23izb1cypiag4lsrf8v")))) + "07zs9x5fzxzwicjc5x29sv33yidmq1ar70ss91py094zbw9i63qy")))) (properties `((upstream-name . "Spectra"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-fs r-iranges + r-metabocoreutils r-mscoreutils r-protgenerics r-s4vectors)) @@ -10617,13 +11601,13 @@ data sets ensuring a small memory footprint.") (define-public r-stager (package (name "r-stager") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0advih0g2g5w8bx9f21chz8a66f4v84qn3p5skxi084pp142v5ms")))) + (base32 "064hvx8qyw5hdhihwl9k0jqhg6saz4ng2m37d2ipr5pz9v8adspb")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -10640,13 +11624,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1c0m9k3gjmj160k8xyj2r60lpx4qgp7xibljfg8ljxr33f8aqyaz")))) + (base32 "1ffn73sx0qbzbh8cjil9r159g0fjnvi6y8rlbg6nf7p3zx3aya54")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -10670,16 +11654,50 @@ associations. Each interaction is associated with a combined confidence score that integrates the various evidences.") (license license:gpl2))) +(define-public r-structstrings + (package + (name "r-structstrings") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Structstrings" version)) + (sha256 + (base32 "10j1khhjd30wn9yfz4jhgx34z0yyijgwgydr8ric52337vwpx6dl")))) + (properties `((upstream-name . "Structstrings"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biostrings + r-crayon + r-iranges + r-s4vectors + r-stringi + r-stringr + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FelixErnst/Structstrings") + (synopsis "Implementation of the dot bracket annotations with Biostrings") + (description + "The Structstrings package implements the widely used dot bracket +annotation for storing base pairing information in structured +RNA. Structstrings uses the infrastructure provided by the Biostrings package +and derives the @code{DotBracketString} and related classes from the BString +class. From these, base pair tables can be produced for in depth analysis. +In addition, the loop indices of the base pairs can be retrieved as well. For +better efficiency, information conversion is implemented in C, inspired to a +large extend by the @code{ViennaRNA} package.") + (license license:artistic2.0))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb")))) + (base32 "1h3l3xbxwf2w2dl0qz72v68h5g77zhd2rr0g86l2dhn67mhy8ml2")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -10710,13 +11728,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.30.2") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "05dy57fi43rpq9bhbsc4apa62xki99r84098pbvi3rjmac811425")))) + "1949k2658drmcrrr7v6748b40g2qym39n0ch50jxf0xmmlb1r04z")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -10745,13 +11763,13 @@ samples.") (define-public r-survcomp (package (name "r-survcomp") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "survcomp" version)) (sha256 (base32 - "1va0ijx3qk3rjhzaflygfwlzn5a670y833qly8in8p5r3al9bdj6")))) + "18a81vv88xj3frkdy5l6w2fc4xzr1k6vgbz4j4marlmh6mz6skin")))) (properties `((upstream-name . "survcomp"))) (build-system r-build-system) (propagated-inputs (list r-bootstrap @@ -10772,22 +11790,22 @@ of risk prediction (survival) models.") (define-public r-sva (package (name "r-sva") - (version "3.48.0") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1f6ia57fn2sn7c2zdfswvj9kx8xayssrgf5q6hrr9nrxc0jq19g3")))) + "0p4zgw1pi5vnaqxn6jmvhpy0h5hnnqp41n0k2v0chhqgqxgn67x1")))) (build-system r-build-system) (propagated-inputs - (list r-edger + (list r-biocparallel + r-edger r-genefilter - r-mgcv - r-biocparallel + r-limma r-matrixstats - r-limma)) + r-mgcv)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -10803,14 +11821,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.6.3") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "068rikfq32awhvj0abl30bghv5k2z4zlfkbxpmsdapxhmdzhgnba")))) + "01amqib9ahrf19xpy4ivlsss82zyp3w7fbgwrwp53zfbg0cninga")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -10846,21 +11864,21 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "0avjjvih387qhw8n4vjz4jq66q7sicgacsw53b85lq2c6ppib662")))) + "1sznyx11kzw8d8zg5ynl9sp6m0daf2yw3f2b24maxbpr1xkif9nx")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi - r-dbi r-biobase r-biocgenerics + r-dbi r-go-db r-graph r-lattice @@ -10879,13 +11897,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1")))) + "0m6avd815xcv3py5sym083pdccvd4crdyyc7sfpxccnksgchyrf2")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -10938,15 +11956,16 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.46.0") + (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm")))) + "0l9xkrvsrc3m65kdjcyir6jkpa718g7idziwr0pp5yaj84bd3xia")))) (properties `((upstream-name . "VariantAnnotation"))) + (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase @@ -10959,14 +11978,14 @@ R, enabling interactive analysis and visualization of genome-scale data.") r-genomicranges r-iranges r-matrixgenerics - r-summarizedexperiment r-rhtslib r-rsamtools r-rtracklayer r-s4vectors + r-summarizedexperiment r-xvector r-zlibbioc)) - (build-system r-build-system) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") (description "This R package can annotate variants, compute amino acid @@ -10976,14 +11995,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.68.0") + (version "3.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0i6c0wyhj0gcq0mw13zyk60cza2baq4yrj1n2dzqgsqkmhm5lfla")))) + "0li0yxf8m34xpmrgv5vciy8zdsbfdlajl9cmnxr4g4nmarik2bkh")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -11045,13 +12064,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "1byk8xgn9rwfbi677b99ysxi4a9n58fr3hbnwjzhnziy2n2cd703")))) + (base32 "1cnw2zbjfs8qcgqrx557g00m59h5pldcx788v9r4gn2f70rx7vx3")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -11081,13 +12100,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "09pskmhjymqvhk26mk5yy1k195v536a2qp4k6xdd67xhf5ag260i")))) + (base32 "0pby2h8m12xlngpk33dvh3nkrpgqi4f2mb7g9jafyiv3sl8pjd19")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -11108,13 +12127,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.40.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2")))) + "0h03imdl0pyy714kmddsdnsv69bd8kr7bhi9wq9z18y8ahg5cqx1")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -11131,7 +12150,7 @@ describing each of the graphs.") (inputs (list zlib)) (propagated-inputs - (list r-biocgenerics r-iranges r-s4vectors)) + (list r-biocgenerics r-iranges r-s4vectors r-zlibbioc)) (home-page "https://bioconductor.org/packages/XVector") (synopsis "Representation and manpulation of external sequences") (description @@ -11142,13 +12161,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0x3d5kihckqnfjkc7dxk6mc194vwwr03jfjx2qh15g5494gfmm53")))) + "043xwgw3yclxnxlfl7fdwf7qf7fajzvqdv34qxnngxj9wpgha3gv")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -11161,13 +12180,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.10.1") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "1p89i2dfwcgrdchdnxrywp3jjjn5jjs5bisrx5kav26yh2pyx1wk")))) + (base32 "029bqn25c90algvgacxbv0fdznpg879xjwfj5hiydfwq30y0kr8r")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -11193,14 +12212,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "03x90l7rvxk0z03p5immqbyyhiygi3mkik636al1cjdcxl9dr5f8")))) + "0zvb84jlsvmr2dvwyy4xjqv353qrxpls0v2vz0nmj1q4m7lrpl1k")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -11209,6 +12228,8 @@ saving AnnData objects to disk.") r-biocgenerics r-lattice r-rcolorbrewer)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description @@ -11218,14 +12239,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "0i745q2kx7rdfbkz3cwzzp1m4diny25mc301vy0sh4z5lpi5mdm8")))) + "1gdvjvyjfpvvrqyj9rq1l4dnq00hr8vr8knnlb9gnjk21sbcf1d7")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -11253,14 +12274,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0gs26h0hm8xlv3aayz4w0vwmw15x5602g02728spsm3n0qra3b1j")))) + "0pqn5qslynylx235wknwj71a6j7xf5i6pb7wjm00jwrdbqwvdlp6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -11289,13 +12310,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qfeatures (package (name "r-qfeatures") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QFeatures" version)) (sha256 (base32 - "1xnmd14nf4cqbfxkjsl6af312k7l27ars5g8qdnljylkn8kq276z")))) + "1g744fpb6g690bjbjs4v2899wwv6qc7n5cyq977pm8f3wln0m7mx")))) (properties `((upstream-name . "QFeatures"))) (build-system r-build-system) (propagated-inputs (list r-annotationfilter @@ -11324,13 +12345,13 @@ proteins) in a coherent and tractable format.") (define-public r-quantsmooth (package (name "r-quantsmooth") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantsmooth" version)) (sha256 - (base32 "05lja0viz5jgc7g3b8qfhd1x596vczid0dz8278qpl4zwv9i17vx")))) + (base32 "050nnwhxk3ld615f6ij4cc3d6wzrrxykvv02fr20fg5gzdj0z08a")))) (properties `((upstream-name . "quantsmooth"))) (build-system r-build-system) (propagated-inputs (list r-quantreg)) @@ -11351,14 +12372,14 @@ on the location of the probe, and other useful tools.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1552390pf3wrrir6c9xshgll69a33fhbdnh2cvpnznma1ag490ki")))) + "10v5khnrs1fa84d430zy52f9466rwb1byaw1l3c9nivbhmaxhvyi")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -11406,13 +12427,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apcomplex (package (name "r-apcomplex") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apComplex" version)) (sha256 - (base32 "057p1bsqqw3r49bsx78prqc4jha468bfx50gpl62giix0cfs007f")))) + (base32 "1y3c3358y7ynn5lj2gcy9ll2gxnnlv689pj0bgr2gsnhbss1kw1r")))) (properties `((upstream-name . "apComplex"))) (build-system r-build-system) (propagated-inputs @@ -11431,13 +12452,13 @@ spectrometry} data.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7")))) + "0cj9yzmh9w3fk3rxmk2k5j55r42mmz9znszmr4l160mr23alkzx4")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -11458,13 +12479,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0z89yikglx077x18qhq6f8f2fa9xni12jz8my9p5sa6zmvnj4dnm")))) + "1k974cvfbkl8ffn7k2la843bv2pf33cr5f6fahiiy24d68lxwifr")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -11485,14 +12506,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.10.1") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "12frl2wfvfz4gpq4fjsmglqyqfxdk3zjbhqkc78rzylbw37xx3bf")))) + "1nlcx4fl1cpcg38cn9p55f75bv6pcg6h2jv4z94g2b7g1gwjd686")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -11563,13 +12584,13 @@ processing to visualization and annotation.") (define-public r-mbecs (package (name "r-mbecs") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MBECS" version)) (sha256 - (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz")))) + (base32 "1j7vb26n2fnf5fkk8hfz552yx91g4zg719alhg4hg2vvjd1qx2l1")))) (properties `((upstream-name . "MBECS"))) (build-system r-build-system) (arguments @@ -11588,7 +12609,6 @@ processing to visualization and annotation.") r-lme4 r-lmertest r-magrittr - r-markdown r-matrix r-pheatmap r-phyloseq @@ -11614,13 +12634,13 @@ before and after correcting for batch effects.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "0c48ycgba1m10p1w2qz9r7yxw15nqzlz8fp44d6lbrvj3svmgjwi")))) + "1x7azijfs28iz2w40b9hnpgwh4jxgihl8cj6h91b2wgz79sq649l")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -11646,13 +12666,13 @@ large datasets, including support for on-disk data representation.") (define-public r-multibac (package (name "r-multibac") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiBaC" version)) (sha256 - (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i")))) + (base32 "1mwfibakrxgs3r572bqqqmzq7ys6cs0bpn0wfrcb08ww2197xc4j")))) (properties `((upstream-name . "MultiBaC"))) (build-system r-build-system) (propagated-inputs @@ -11676,17 +12696,17 @@ the batches considered.") (define-public r-multtest (package (name "r-multtest") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "19c6l8pkyp0m2zdzhr81cnmx5lqf501sap9h6ig5iiv66sf2ysmz")))) + "0s8x2rg2xp6awg2cikybgxrxpi9f91jah7dskk5dnfkazd20di4j")))) (build-system r-build-system) (propagated-inputs - (list r-survival r-biocgenerics r-biobase r-mass)) + (list r-biobase r-biocgenerics r-mass r-survival)) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description @@ -11711,13 +12731,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "184izzxc8bpagcac8wqinjp8kmf9zpvjibl0g32nnr64kp9f4rsn")))) + "0p7g7ykpkngbs3h1dsackfy93l8lvc301lr64ffsiaw60gllcx01")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) @@ -11754,13 +12774,13 @@ fitting of some classes of graphical Markov models.") (define-public r-ggtreeextra (package (name "r-ggtreeextra") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtreeExtra" version)) (sha256 (base32 - "19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr")))) + "0q8k81mq5q9fym4zyrkzapgyww23lkxpkyj2s9r1y0ciclk90zdc")))) (properties `((upstream-name . "ggtreeExtra"))) (build-system r-build-system) (propagated-inputs (list r-cli @@ -11785,13 +12805,13 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl")))) + "0zjlsvzl2f74fvqw4ijnai23qwhlcpgd5p8z9dclnwnsgdbm6hcq")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 @@ -11854,13 +12874,13 @@ a given recall, F-score for single and multiple classes are available.") (define-public r-pepsnmr (package (name "r-pepsnmr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PepsNMR" version)) (sha256 (base32 - "17rbadvay3kbp4r6p023yww4biw9cl359q200ciygr7d2ffcas85")))) + "013jw9l7r87j4bmpjrvq5qn91kp44wj5vd68cl5axbqhjg7fq4ww")))) (properties `((upstream-name . "PepsNMR"))) (build-system r-build-system) (propagated-inputs @@ -11910,14 +12930,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.34.1") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0y9qskkdkl2vdbn66md4xisny0i7g2biasylp357vrkv41d3al6l")))) + "012hhakhk81qk1hi4igfa4vji678gmyvdxi05z9mdsx721lwwy2i")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -11964,13 +12984,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "07hrafzn3787vprdwdk3cfyhi8df7hjvxg9vq7ad8raqzb37lqil")))) + "14x5jib5xh2006lg96v3b9n2pnbjcbsd5igqybqsv0c53rk9394d")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -11991,12 +13011,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1z8fx47ng1av8nfpk0i7wpb8k8lsrn66k613p36mbh19m5fx05ks")))) + (base32 "1gj4mdbni5fk2z3zrk2cnhy610ihhhwjb9l1crglkklwxhkqlkvd")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -12010,12 +13030,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1r050acahvfp2ib88sy9xj4yjzy2d8h73hndi1s075h0zv12mjj7")))) + (base32 "1iw03gq1kvmn9a6h0kw389l9i7h99fbxcsag9f3gkfznjv0vp5k4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -12029,16 +13049,16 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "02d8j0al062k33h6n3ihn7kwbqp3pjwg9zzbr45ay1m1jm6bappi")))) + (base32 "1x2zfr40bm42zd1bljwpbz3cz1q23a3yy1g277lwsp78gxbn3zly")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs - (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall)) + (list r-biobase r-cghbase r-dnacopy r-impute r-snowfall)) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -12048,12 +13068,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0lcf5zkv44s7xsa2svxia7inv6iz2k1kilfj5zcq80r339pj3vx4")))) + (base32 "1n2qngqqw3hfv1yscksnpg8wslc85dlvaqw1hz2qvsxf1gcq2mks")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -12080,14 +13100,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.31.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh")))) + "1b5vvzl0kkm6kb03vr6m6sdlr3azpc24933a7ayxkiffmf2wbi0g")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -12104,14 +13124,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1v27bqik5cgcvs1kb67s52r56v6fakvmi81iybvvvbxvcn1dmy9r")))) + "061d2z1rrcyad6cf19si14ab9a3dxdi17sfbkx3vx8kdsfs3djy9")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -12138,14 +13158,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0qgzq82v4glkc0krk81zj9z71cnrvflsf1w45r9zmaw6bq45rfqd")))) + "1bd37ypxsj9p94p2851hhc9ind59b5pkg1lyalha1nfw5gf8iay3")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -12179,14 +13199,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.32.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610")))) + "1cigbp3pc70ipja9mmprkrs91723r1zwgxbzyp87n5mb0i4q8xqh")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -12207,14 +13227,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "1vs3mqf3x8zk7p83jkv41kag1bmn5zxrr3j1ldqk6wxsl77h55c5")))) + "0mpgxcwhb734pyn6bj93xknb704yrjkprxpa7kqwl24rbqyjydqs")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -12241,14 +13261,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0qhb2mm5nynnw0cj5da0i6hb1bz7cyns0gp7xy0wscmfyh2wahbv")))) + "13rnxig22agykzv3q7wm4wr9c5aw56q6q1zv8m5g5ngjcssy8l4c")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -12282,14 +13302,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0ph22v1an2havnh9sm7hms0q2pq4fjad2cm4dffiy3344cv70sn1")))) + "10a83rr0qhnzdhvlbyn0y690hxnl8q86z47dpimr6sq41w463im3")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -12302,14 +13322,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1r13n64s9fbx951yaa4mpna71vynbkjz78irk96yzh2x2zzxpjvx")))) + "0waw5hhxh8yab8fqw9gnd3l39s6wkmp8690rhs4llarpqz6ssrhk")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -12328,14 +13348,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0171wizl516chzzwnbc2z2bf5sk4a491fcs4yhq5ycqaqpjmbg35")) + "0pkh15jjjb83pq7d49yzwb2gyc95x4rww78qnzpdrzhycgmcapii")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" @@ -12413,13 +13433,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "0d6q8vn8z90k8ffskcn9jmgg5x5pfb3wjv67bqskasy38inn1zg7")))) + "1qc3f1spzkcjk95b07jpxgrjiwmlamwwx6mlhml4lgzy5qby7dpw")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -12449,14 +13469,14 @@ experiments.") (define-public r-rots (package (name "r-rots") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "0b2fl4wn696ia2kxihc6088ncnvd87ffq40bz58qi1bhq6krcmwv")))) + "1zd5w3mq0vjs3ivdb23x6d28sqq0dsfv13d64k1yijr4vdk3wvp6")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -12472,14 +13492,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "1kzrscaqsrsvdq2c9g93l7bjmv1s5p1l3cbrz6skkqls9h4gsw08")))) + "0s5hia3xvddi0gaawcr5zsh34v6sh2zdi5gsjis8ar2g2p7agqgg")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -12496,13 +13516,13 @@ genes or proteins in these datasets.") (define-public r-plyranges (package (name "r-plyranges") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plyranges" version)) (sha256 (base32 - "1qv8snpcxpg16v5ji7sq3bnmgrgghz9h4mh246mcnnxfhi44b6nv")))) + "1z4pc9slbd6ji3c6g9flxhvvf0anjmywrlnjblv1mpgsh88avp7w")))) (properties `((upstream-name . "plyranges"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -12530,14 +13550,14 @@ accessiblity for new Bioconductor users is hopefully increased.") (define-public r-inspect (package (name "r-inspect") - (version "1.30.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "1nyfl78fjj956bk1xf32k3jdqhlffx6grbl7vajn48q5ldsx8kcx")))) + "04znack6p50cmc2qyk4hf45m6v70p0bv7h3xs87j0x0h4mb920ch")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -12546,7 +13566,6 @@ accessiblity for new Bioconductor users is hopefully increased.") r-biocparallel r-deseq2 r-desolve - r-gdata r-genomeinfodb r-genomicalignments r-genomicfeatures @@ -12555,6 +13574,7 @@ accessiblity for new Bioconductor users is hopefully increased.") r-kernsmooth r-plgem r-proc + r-readxl r-rootsolve r-rsamtools r-rtracklayer @@ -12576,14 +13596,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1jys0lj92zkqa3bb22fg35q5y8ij5pqhy3yvzg8zc8bjpzdvrg3a")))) + "12x4k55kshvwyzl83zkgkp0ylryr8wd3kz44ngp60k4pkwhkl9h9")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -12603,14 +13623,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "0kxaaqf6py7kfndgpd0faxv6g610zj16pyvn9b4x9s3b22ib06j1")))) + "04byggwsvmqrl77268smbas0wax460cdshmp4v5iqc5fghl7n0p2")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -12628,14 +13648,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.18.0") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd")))) + "0lvsw920i75di5pwq7yvk8wcxp01wrh7863xmwbrmk5jrvl3y4h4")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -12656,14 +13676,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0xhw77w28r3agv0hw7fjpn1fp2p9bz7kdzwzx7gsa8411nffmd4d")))) + "1aigca0s8cmi46458pl9p9vwlkrmqawbgi0xmbwslz646x2s2h4a")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -12682,19 +13702,18 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.24.3") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "0shm0mdqvsk5qipdqbz3251kks6ii1vpx1pph0ms271nzs6fcvif")))) + "1kvzdryw74r74gwxddsrng81ww49p3s7hgxn8ggl0p8fvz3sfgir")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs (list r-ape - r-cli r-dplyr r-jsonlite r-magrittr @@ -12715,13 +13734,13 @@ platform for merging tree with associated data and converting file formats.") (define-public r-treesummarizedexperiment (package (name "r-treesummarizedexperiment") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TreeSummarizedExperiment" version)) (sha256 (base32 - "1grnz82a7l5dpwssc24yxhllqdcvza2gc4h4cc6zxjcdg5r4l1ra")))) + "1yvqixlivapasx0ircfhmc8ckr7sw86d9vfvnqj97p4r667x6z6g")))) (properties `((upstream-name . "TreeSummarizedExperiment"))) (build-system r-build-system) (propagated-inputs @@ -12748,14 +13767,14 @@ data.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.8.2") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0l8llnvmg8k5qgag6vfgx1gdv0x46p3ypfz5apv23qhlbx4jfjja")))) + "12w2l1q0c5aznd5fls04wvgsmjidqhr1kkqj4gajz1abj9f49cqf")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -12786,14 +13805,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.8.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "0lr2sgbgdbqq626nsm3vyhghs8nalg5cxycr4cwsqh9nqrmip3wa")))) + "05cy3xvj78n2p9l2pxfys7aczr51gm2ywprn4qmzr7ppb6rq5f66")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -12815,14 +13834,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9")))) + "0z1p02329wk2x058ij42q5pyvp0vhsihaxmizgzcj4sww6i28j33")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -12850,14 +13869,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "0hc85dq68h7dy5jcflpjj05231ny7na9i4lksfsw89jhmxgzhacd")))) + "06xwyqlsas98lxmd0qw5ysjwbk397kyapd5jq5pzjrynsj4r9xn6")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -12915,14 +13934,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1iysqs2k0xxiwd48ymahf6rywwj9ingjcfmnhx9d1x6w2h00v7lz")))) + "04dhkm8cq87x3c9f114z6q1pcw77xgs33rmhgzk4ajzxywhklq4j")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -12975,14 +13994,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.74.1") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1bj87ksvch5cm5zxwgfiiql0j94pvzbpn59wp6bacyip65z7w3ax")))) + "0hyjin75v8l2a8qymsd6rjb8m7svv2q07s6z1dllqag09wja1yfz")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -13073,18 +14092,23 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.40.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0y23k607f61csj2ciaqnl8pzsjisqlcnnhlasv36446n8f3silx5")))) + "07x9fh8akgiixsv1xddkvs2q8xxfsibas01kdx0kw6wak3nihn4w")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs - (list r-blockmodeling r-gplots r-testthat)) + (list r-bh + r-blockmodeling + r-gplots + r-rcpp + r-rcppeigen + r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -13095,13 +14119,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1nqcm2jlazm8wsa4p6a59m1j8y1qdwg0w3kii4dqnkann3q2q68x")))) + "0jr9lp250s9066hh40vxb6c6yhdd8yrnk0zklwylkf3jpbdgl621")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -13133,14 +14157,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "08b4d7k5qx19bpg12pw89ckk8x6r2n28qjdxbmy1cxn6dcgzhijd")))) + "1946wlw9zvyxdd99rs2rliks54ff5dkibavxd48aj7cqjsjh6b7g")))) (build-system r-build-system) (arguments (list @@ -13155,7 +14179,7 @@ coordinates.") (inputs (list zlib)) (native-inputs - (list gfortran pkg-config r-knitr)) + (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -13172,14 +14196,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0i4yahgkrg9rnc0xldm026k6bd1bn5nkgkaf6kpyyday41rxzyq8")))) + "1pix38lg9snw0jdihh8sifnmckyw1lniwp95r93ca524g6swfc8b")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -13201,14 +14225,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "120bcakhhl6xqsfclzgmn7rcxmld289bjl6j7nrli7aiq5ilz8h4")))) + "1f0j10wha60vv592vsnv2pcqwz7g2fkld8pnar9rpwwb7qd0wcnf")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -13238,14 +14262,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1yay0i0nh2ax35ayqlpnmq0839syl5991hacyrbv3li3gqjc9qqv")))) + "06py71xbygfwq55kawh2x340idrf5mmxmnsz5m6lph2ka086dc5v")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -13267,14 +14291,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1cswij2mdjsdh99rmyh68wscg6h7cs0cff69gnki4gzzjfxy8x3f")))) + "1z4ddkdd3mzqg0c6l94qmrdwrm7427k5xiwzgkzx43gh1j4911d5")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -13310,14 +14334,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "0vm7v2anbrci6mcans9y9svd6xjm4waf2kny3rz0cjgsasw60ycx")) + "17iycxxp6jb56ra21546kh2zlrm8by2vrlvsxvx8xmbpk32fb4lp")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) @@ -13367,14 +14391,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "05pix638s4hkig2i048m5jjhvw6cqr2b5qvfkk14i64p9kpifmqj")))) + "0i1qnmiaf3gf8955nlqzd81xzg4siliq154k699jmsz0fyyykia1")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -13458,13 +14482,13 @@ several functions from the R igraph package.") (define-public r-sangerseqr (package (name "r-sangerseqr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sangerseqR" version)) (sha256 (base32 - "0hhq5zsx4srd9ndr370m44f80qdlrqafjv1838wf65gzijffhfqb")))) + "1vggjvxfmmm2gcyfay22wahkib15i164ic148jdps36pxapl6hi3")))) (properties `((upstream-name . "sangerseqR"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-shiny r-stringr)) @@ -13574,14 +14598,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0cxhy4yrww6bh4z603389fikhix8rhfy04ylhm74fdmdng4jblg6")))) + "0qs0sc47n3p9wmf5cmc39cb30i8pbsyizhr29b3ld197pi1ba5wb")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -13600,14 +14624,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "1ndb1zcbdy00xkfx18slrm5bnld9ci5scysc37clhsq2lq5xb25z")))) + "15hzsq8ckw8v8ccz30kia9qr1iymmcszc9z31g5arrx1y816zgbq")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -13638,14 +14662,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "0v3rd2h0n52qz9kqxa3l49rjfssfk252dy7j2nvi34y85win2p1w")))) + "1y0blhh75hb60h9jmvz2naqfzky4zgw5gn81fbj74jfph9y712lp")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -13682,14 +14706,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1xyrfj8b7j2wdjlbmwhx1c0hfbvr7l7jxyw2v64fbw8604zprv4s")))) + "1xjfh9lx2cfwzkk61pdarajsa86nzhy3dz7r4zws20pz4xkhwv87")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -13717,14 +14741,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "190i3b9qmh26bic1lzi54mw4p1nrg57qijl1pg6b29w3i6srq692")))) + "15i47b995dqh0dlg60lss5vgj31as3cwhb2z5fqbnknx3lj7s6rl")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -13738,14 +14762,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0h5asj2w4xgfj9xapjawmxldnhq789py39drlr8illyhcczkzkbz")))) + "0jzxwg28ih1i0f7hal99g60zply0g613b4wrjsbv738cmlsai2kc")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -13762,14 +14786,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18")))) + "0vnm0m9abf8478f7lair58vw1v4mxj8sbmrxcpf8622ygf2na4qc")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -13796,13 +14820,13 @@ studies.") (define-public r-bumpymatrix (package (name "r-bumpymatrix") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BumpyMatrix" version)) (sha256 (base32 - "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i")))) + "0ic87fjxwb39nmys09zb6k3ghcx8mmmj9pifljs10449i2lgzl2r")))) (properties `((upstream-name . "BumpyMatrix"))) (build-system r-build-system) (propagated-inputs (list r-iranges r-matrix r-s4vectors)) @@ -13822,13 +14846,13 @@ data in a format that is compatible with two-dimensional containers like the (define-public r-mia (package (name "r-mia") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mia" version)) (sha256 (base32 - "1p78yacx0cgihva7m2n3vnll5w4b47vl98hy12pq9rnmhk6r591z")))) + "044spfxsf7xijnbh0933cwdkycmg05zsfqhbx5pkfajysh6w5cxp")))) (properties `((upstream-name . "mia"))) (build-system r-build-system) (propagated-inputs @@ -13836,6 +14860,7 @@ data in a format that is compatible with two-dimensional containers like the r-biocgenerics r-biocparallel r-biostrings + r-bluster r-decipher r-decontam r-delayedarray @@ -13844,6 +14869,7 @@ data in a format that is compatible with two-dimensional containers like the r-dplyr r-iranges r-mass + r-matrixgenerics r-multiassayexperiment r-rlang r-s4vectors @@ -13870,13 +14896,13 @@ summarization.") (define-public r-microbiome (package (name "r-microbiome") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "120wyjv2r9cbjgxbp70nzf249hai8cqn59gcbgwnazynfy5ih1w8")))) + "0xmkwf7v89nwlpjrzqxv87lbsn6za99v7f0yxkgzfk5n6fadrf05")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs @@ -13941,13 +14967,13 @@ experiments.") (define-public r-milor (package (name "r-milor") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "073s239aqkixsrarqxfv4nmpcj025k32nhql63qaxrkrvvdd34di")))) + "1hnvw9x0xwjb0br4yvzkzn73nvm8p3j3wmcw8jrid105j0fz6vcj")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -13989,14 +15015,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "18b9yg9hnnm1saaiprm2hj86aajjwm1zwvpj0yadfa3s811pw4nq")))) + "13lldzj68vmmmrp5fi2rfxbchbivaa1scq56hl0v9mxxicw72a0x")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -14040,13 +15066,13 @@ methylation arrays.") (define-public r-missmethyl (package (name "r-missmethyl") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "missMethyl" version)) (sha256 (base32 - "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h")))) + "1nv4rm5pbx0s7m5zak3jzmwz4pkf8ghkj0ckdcsnmw3k364ny856")))) (properties `((upstream-name . "missMethyl"))) (build-system r-build-system) (propagated-inputs @@ -14090,14 +15116,14 @@ into account multi-gene associated probes.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1aa0pwjyp2p9a4mx4n4qw88ndgrj56p669yzdkd7hxhc3x55nzlf")))) + "1vracrvy56kk3hc9midxdaxhad2zf1lspn0zzxjjbsyzx3r0ip0n")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -14137,13 +15163,13 @@ and Infinium HD arrays are also included.") (define-public r-lefser (package (name "r-lefser") - (version "1.10.1") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 - "1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4")))) + "0aywwinp4wwwa12rq60gpfk5gn28zyimayxakgj4lhfwjk0byz8m")))) (properties `((upstream-name . "lefser"))) (build-system r-build-system) (propagated-inputs @@ -14161,14 +15187,14 @@ to find biomarkers of groups and sub-groups.") (define-public r-lumi (package (name "r-lumi") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "1lxxqr7x9jdjrsj5j95jb0dbd7p208vifxw3j4s4140zh1ppxnpj")))) + "0iwkag84w1sc703jcdfx0h799hlchdiqvlps8g8lwmil5b0xlsw5")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -14200,14 +15226,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1sqkmjah2lxahnvwv04a970za2b8kzvmxnb41k9xrnvj0akigc2d")))) + "1ax5zmby8zw0mgxjd8yhlk4ai0s03zq59qwzqgv8zqlms8yjpvs2")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -14261,14 +15287,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0")))) + "1y595hq40kpsasp74wsbf3ngd2rrriqg65z9y4svcwdygj03pgrz")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -14357,13 +15383,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "14b90x9h34mhbc4sdpzkygrrswf84pi1ddwpzxhvlvr9gs443xqs")))) + "06k0jib20nq7zqc5vbgag8v1lbadjlg0idh5jwn5bcjc74dx15vj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14426,14 +15452,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47")))) + "1ibg4cdpbv4ph3y4r90j8zfwr1cy1z33p4bazhzyi2zv3xa1nrq6")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -14466,14 +15492,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.8.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx")))) + "1vs7x4dc2vrfi2wi300bjr2hl1wwp4v27sgzycr6qv6x2nx9i5xq")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -14491,18 +15517,18 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9")))) + "10jhjzgf10w9cmr97qzc3mqvgvgx9h7pqk7zkkqwhg7anv6wa788")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-go-db r-rcpp)) + (list r-annotationdbi r-go-db r-rcpp r-rlang)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") @@ -14518,14 +15544,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "0ic12p1qyfrmh3l1wv7s9yi8sr84crj4nksmcx0lybb6rak9gy0x")))) + "1b1r7jwilwvl89fw3rqascyhy8wnm8y81lnx85pwjk55ld56jlb1")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -14548,13 +15574,13 @@ the data set is suitable for such analysis.") (define-public r-anota2seq (package (name "r-anota2seq") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota2seq" version)) (sha256 - (base32 "0pmk45276bl3qppzxlp4jpc8bsvdpca8nzrdl6c4n9r3xhzfpyq0")))) + (base32 "0kyxwhj5vq5z4v3x3hfb9ks3h37axqskyj9rzyj2bzsy2yk9hajn")))) (properties `((upstream-name . "anota2seq"))) (build-system r-build-system) (propagated-inputs @@ -14581,38 +15607,16 @@ mRNA levels or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels.") (license license:gpl3))) -(define-public r-sigpathway - (package - (name "r-sigpathway") - (version "1.66.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "sigPathway" version)) - (sha256 - (base32 - "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy")))) - (properties `((upstream-name . "sigPathway"))) - (build-system r-build-system) - (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") - (synopsis "Pathway analysis") - (description - "This package is used to conduct pathway analysis by calculating the NT_k -and NE_k statistics in a statistical framework for determining whether a -specified group of genes for a pathway has a coordinated association with a -phenotype of interest.") - (license license:gpl2))) - (define-public r-fcscan (package (name "r-fcscan") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "071sylwwj27bk39pkn5a29r7bmfpmyaixkkg7dqcdq230c1dsrps")))) + (base32 "0hhad9vg43j0yz8fp2w7qdhvdy77yr7anv0fi170042x3piq1q7r")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -14639,14 +15643,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0chnrwiwk31crrx4am1yrbxjdqd3jycgjgczqzj7lxaa9v7lvm7z")))) + "0sykd4ingpw41615hbr3vw9yd1ks225hdb5qxnhbk4m4wxj814ql")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -14672,14 +15676,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.26.1") + (version "3.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx")))) + "0kk4l8cxyvcq4cjjnb59zajf4ci0igml13582qqn8123cqkbf8pf")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -14690,7 +15694,8 @@ to multiple hypothesis correction.") r-gosemsim r-hdo-db r-qvalue - r-reshape2)) + r-reshape2 + r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") @@ -14707,13 +15712,13 @@ data.") (define-public r-enrichedheatmap (package (name "r-enrichedheatmap") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnrichedHeatmap" version)) (sha256 (base32 - "18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya")))) + "0j87x26qimsx4gi311bm1g9bldwq9r4z3aflxf8p91zlavjbv8zp")))) (properties `((upstream-name . "EnrichedHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize @@ -14739,14 +15744,14 @@ correspondance between different data sources.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.20.3") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "11hgxs42wvirv6b9ywr2jb51s67k4r0pm21dkvm7xjbsbarlkhmh")))) + "05ps96adbn4h8i0mqflzm1h6chjlrmfz6hx393232bhb995jfllx")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -14807,14 +15812,14 @@ attempts to assess their statistical significance.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.8.3") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3")))) + "1vlrybyczfci5qnw50k0y2j2853r2p1ff5bpj35rdca4ja0iqh2q")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -14827,6 +15832,8 @@ attempts to assess their statistical significance.") r-go-db r-gosemsim r-gson + r-httr + r-igraph r-magrittr r-plyr r-qvalue @@ -14845,13 +15852,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706")))) + "1qnxrdpp75m342q4chwaig413l52giz1h7nd4p9y4b472dqx9hh4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -14891,14 +15898,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.80.0") + (version "1.82.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1s5b27n01crfzrpshhiv6g0q0qf0dip1gw4nkrkg5sh5x9dsikq6")))) + "0aga7xhx5d1xp09n2im7yqi9y1b3v22l554hi35ahg2lwwvxjiw1")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -14935,14 +15942,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0jy3qk31lb11bixncb2w2hw1ibvik31bfi2l5vyq5wjyxndfyax6")))) + "1mdv0x9lnr0bm96h5f9104nqg2j6cjqvp5prrxx10j0d6464vmkw")))) (build-system r-build-system) (arguments `(#:phases @@ -14967,14 +15974,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "14q9q3dxnmmm491af53hd0dwwqiz47xxrwy05axh85x4fh01j3xx")))) + "0iismcsnkyb7m4dwmxw5pyvscj2bhp6zw9hpdb2ff91viynbknq1")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -14991,14 +15998,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1z5xypz5jvb06pk71x6953iirhh1w1mggm0pxqibg0ag9lx2zzmv")))) + "1wxkyqyhb3mj04kmaisd09dapywjpc081ihaig5rs04k611ddvhi")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -15021,14 +16028,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1dxh0zbv4z4gqnwbv7yn247gx7cqv68vb43p6f98c2kyqilfpjg9")))) + "19nf3bc0gdwixif50f3bs47a1kw1w1lir1dz4l8zqdp3h8gfmj60")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -15045,14 +16052,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "0lx7fx2vlpq3c347gx842qlcvnzl0r25i5a55l0qbf8rb5liq2yv")))) + "16lgbwsgwp77x9a8c3hr1aqhp36skzz72xhbzm0a7w3kagmd8gn6")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -15069,14 +16076,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "01c8rps321820b0pchfqv8shglb26rys7hqkwygpzzx3jj310v8x")))) + "0hin5lpwa7cxa862jh3y7d8kq3q9bv76ri08b27jxzyr5p7xwcr2")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -15100,14 +16107,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0n49scwwmg51gcakbc0bfjcy1lcpdxg974l11yk35kj0bg9ynpgi")))) + "1hdqnipg326z2k7vs6sc1brc9lvvhmr2l6cjp4f9a205g4q7r9rr")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -15121,14 +16128,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "05kcwmv3d59lrdnpi82701biwawnnpfvpwr170xdi3hfdff6g59c")))) + "0s865nahgm0by2nvjydkjlhkj2sxmrvcrhw7rmm46ld4g10xsrc8")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -15169,14 +16176,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293")))) + "065b4xf5i1bx08494nm3r497bs47s5vf99l2g37nlpvxf7pypvrz")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -15194,14 +16201,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "08li2wql2zhg06z0rjws9qcnv3ishgnpc6k8xyjcf7yfyg7qpk1d")))) + "14jcsqb56vn67hjmcjjnwswzbilsarkk8kblc715c7da72q7fzpn")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -15248,12 +16255,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw")))) + (base32 "1z72f5f3sh2ak6zjcfc6j6rblkllmdkli0kb57nwxg2j5hrys3xr")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -15275,12 +16282,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "13fv0rkyb32grswlgzd3zr35p9xpibj2iq62sr23if4w6z5nbml2")))) + (base32 "02i3hkffhhsbzmn97mv8wc2px5caq9xnp45z0l53dp1jxbmms1h0")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -15325,40 +16332,29 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "1g46cxn1h3cqr0yrj6ancshzygiqr9finf1vmmig3h9g0ijgr5lz")) + "10hmqwkysifd59as9zx00p3gj595lwj30ywn9pqb1920q6f5mx2i")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (arguments (list - #:modules '((guix build utils) - (guix build r-build-system) - (srfi srfi-1)) #:phases '(modify-phases %standard-phases (add-after 'unpack 'process-javascript (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "inst/htmlwidgets/lib/d3" - (call-with-values - (lambda () - (unzip2 - `((,(assoc-ref inputs "_") - "d3.v4.min.js")))) - (lambda (sources targets) - (for-each (lambda (source target) - (format #true "Processing ~a --> ~a~%" - source target) - (invoke "esbuild" source "--minify" - (string-append "--outfile=" target))) - sources targets))))))))) + (let ((source (assoc-ref inputs "_")) + (target "d3.v4.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) (propagated-inputs (list r-ade4 r-biostrings @@ -15388,14 +16384,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.12.0") + (version "2.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1z8h9sbr6xqwbsfisr33qdxg0xdrw8r4vvxl1pf4x8vv08zw0vx6")))) + "0rhyfbm5whz4jygar9cqcrfy92h1lyam5wd8d9svhh80f15v53m9")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -15423,17 +16419,48 @@ type and symbol colors.") position-specific scores within R and Bioconductor.") (license license:artistic2.0))) +(define-public r-genomicstate + (package + (name "r-genomicstate") + (version "0.99.15") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicState" version + 'annotation)) + (sha256 + (base32 "1r7z3n6wyrd2cclj5b7sg15wpmjdh9k5b1hjlw7jjx8j384l7l1h")))) + (properties `((upstream-name . "GenomicState"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-bumphunter + r-derfinder + r-genomeinfodb + r-genomicfeatures + r-iranges + r-org-hs-eg-db + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/LieberInstitute/GenomicState") + (synopsis "Build and access GenomicState objects") + (description + "This package contains functions for building @code{GenomicState} objects +from different annotation sources such as Gencode. It also provides access to +these files at JHPCE.") + (license license:artistic2.0))) + (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0mcrkmirss484d2mskikyjdz5cmbhdk52yxkffz9g8g5m9lkq5xk")))) + "1b53rkhyqnyh5vangh3hy4yccx1yackwbv1pxdimbp840ji6d122")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -15473,14 +16500,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "05509xf768x8asqadjj5s50m0yqnklrxi28bmqd22cn6cbmahszw")))) + "1baa3aabkhmwq66xkzf4jk5nz85kkx1ks0mqc91s2ra9916wj6cd")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -15578,14 +16605,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "0dwbh2h2mp8gy0kwqmkri3q2glnzcj8cn83j1qyh7lk15anc33g8")))) + "0g086rj06k3wac24zx66dw1yc1bzv25bmlbjbpcpgdcmyjb1i8sf")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -15603,14 +16630,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1ms3x3x2gvhgllff3nwawg5jlpmgx6dhwll0dghklnv3lssbx4c7")))) + "0p7l856a46zzla8brsg901pmh5738j63h7h7rn3da94ny8k417mf")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -15646,14 +16673,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1zqjmg8nxxj30lxppl685ihynbz44vw7qm3kwjq6cp83c5556hz9")))) + "1d1icbq8i7mwsc7lv9pn4r0vs7azx1lwng5p3ghnray1ygqclbi0")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -15687,14 +16714,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.42.0") + (version "4.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "0z0ajmy1zx7mqcjm2ibyk2qg3cj00kl76padyksbdbmwdncxs8yb")))) + "0jdi5cn4v5ll43xb3l6sy062snd5p9n2nrryc5aqd2ki18mdmghy")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -15726,14 +16753,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "0kjlp62s2393jdwp0crizsgp4iqagbgnd3hdl9vpbr9qrjxg4s7m")))) + "16rdy35wmydcx322pf9j7l7z2mzgrksg1whr8i8xdmdqfnqz3xyb")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -15759,14 +16786,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1kk7ysscq8xdbn35b20s8sn8gl93sy0c718fmvr1yrhiqaxq5alr")))) + "022wn0l2wfizlz6d5plkphjsjbmxw2wcvxrzr4vanczjzzyxv5c5")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -15785,14 +16812,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s")))) + "0s9kjjh1n4a55ycjvcw8ymjcclcj8b35aygx4x1k5af1hf3f7wyb")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -15824,14 +16851,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.26.8") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "16rr2bkni3jx5qskr5fz5lvf23d03xgd3m4068mnd3n9r23hpb4p")))) + "07dxhaywad9ivkrc454hhizfw6a5yvarrc5fp5za2jgsznv408wl")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -15873,14 +16900,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.72.0") + (version "2.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p")))) + "07ina8w8p5bm382v452i2wpmv90gvgli393lsgp7xy0h9in7h6yg")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -15955,14 +16982,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "08m94q65c11isbkx9xljm2bx2aq2rml1bqh5i1cg81xg2ilm9h6a")))) + "032qxwgldl1hbgsgb5q3fi7nfg1nx3k0yppqkvim5cif613m1nzq")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -15988,14 +17015,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0ddfl4jp0n8sb665hcpsij959fl28rj22n1h61wp2374kpc0fwfj")))) + "12d806pyiks5xbvxng4pxn0xqvgs4c526gp2pp2qhdxw0w2m29rj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -16025,14 +17052,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0p5q6nyp8d0gl95rd89xrs08gv87m1q6d0x4ws2b6sd4gc1nw2ny")))) + "0pibk6zdqlbm0rxnb95pd94v6lbg67rwmjnpfxizq7wv36pw6kdr")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -16093,14 +17120,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1nc1imxia71sxxvi77f91yhwxza2l8kk1d7zkp5680xzw6yd6ajr")))) + "044rz2xsz2v8i9ha20hxn2cwf7wa74p5f25jql8ancp6r3gim9sy")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -16117,14 +17144,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.22.0") + (version "4.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "112g2lpi074cr8g09cqwjbcwv9aw4djr7ashxpnxjycd3ayc0j3v")))) + "170s260sp880d3rb256189jvfnnmyzf9nxh8bvksng6yp561r8dc")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -16134,16 +17161,19 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") r-lattice r-massspecwavelet r-mscoreutils + r-msexperiment r-msfeatures r-msnbase r-multtest r-mzr r-plyr + r-progress r-protgenerics r-rann r-rcolorbrewer r-robustbase r-s4vectors + r-spectra r-summarizedexperiment)) (native-inputs (list r-knitr)) @@ -16159,13 +17189,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "06y4pq8msjzwrw1jgyj9yskgpfhvcz54qcsv0h14bakhyrwk00pg")))) + "04wg645c0gww8mq3vg70gqlwm12dmqxmvk704zvmxcpifhrvpn2b")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -16200,14 +17230,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h")))) + "11g6a2315hllf197ssccybhv6i7p48n7bv2amzpgxs7bs7qg3k9d")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -16224,14 +17254,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "15gbs10bi1alxxbxaj4h3hzfgck4nxygy896y34x81w1rn7in3vp")))) + "1gq0hxmnnis0g1y6hiphz02dmk3pfjz874xb2bxqw49z7387fwm8")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -16258,14 +17288,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "03bvh2jk97jj40z35q5n1is2wxrs4dggw08ndyywy4pzx1diqdc4")))) + "1zkc275sb1qbban7sghqziv3xkg7wjdpghddklv451n7j282k6w1")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -16279,14 +17309,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "0z2sixzs0rwdwdhxs5mqzghgiw4g64l8p9ag5lw289bzs4c4kqnd")))) + "1ca41q7hxy6p8kvc3qbjplvn40k4jwhf0mb03njifry4xi1xipgy")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -16311,14 +17341,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1bmxbzpgmwama42a3vi1n0sic166v5zs0kl9mhmrh0rrx0nv303k")))) + "1lp8x9grc07kaz9iy7yc45mk708g9dplsl86fq0ip8rs51c8f31i")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -16344,14 +17374,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1fkzyq282xafyapgi5xi1c2dmfkyikqvf622pycjs80fas38044h")))) + "18pnzc51r7l1ypnhavl83r3gy7l91qnqzvl6771zid04g99pk844")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -16369,14 +17399,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "11h4irhi0pxd0l378im455amqfamqypyl0ri2cs8nk1lg184ridr")))) + "0dx1psk6f27p1kiw4qwj1nf55gpqgisibzipvlnn5m9q3q8g70gv")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -16396,14 +17426,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7")))) + "1plgwi2fmx7bh648fqpzzfqnh84fsgnn5jfcbdf9yia6zzigicql")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -16428,14 +17458,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "001nwl605prg942vmnbb1rwjwgpscpjs27ssic3h10rlmpb65yzp")))) + "1fd1pfw2ggqb0k2npvibfy8liix57m01cxfxp10shvfbzjjy4wjm")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -16451,14 +17481,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.8.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1qk1n50arlk0mfkv9p3zl3lqbapzfkjdbadv51hsp4h9lyaw9sbg")))) + "044kh1rfgb608y2v4wzbzddirhw5crj3k6i28wr78qgnzqc89mdm")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -16483,14 +17513,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1lbkmin9pkk9yzpmwrfyniyqnwmp0wcgiirq8prmzi5mvndl6wm3")))) + "0p56w6431jg921416dkyiykccvr7alq6x6r1gcx5d9hkcpyncks1")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -16513,14 +17543,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7")))) + "1arwr8gisc5g9bwxlachf3lvxpd2767ahnwdf2p1lidwpfism8l8")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -16549,14 +17579,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0qsmy85400in2xvw3bnzjnk8ni3lipqjc81npk3fmvbp6cb85njq")))) + "1h44r0frrw54s9nqa539ifg270ggmm634gj9cyhn4z7nhxxh134c")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -16592,14 +17622,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy")))) + "1pxlpwqzbdii0b1swy9vcq905934yfmyqwfx2j3f7n5n4dgglc2q")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -16630,14 +17660,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.40.1") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "08vns1wbgpxw1x6djp84f9hl3gqaybbw9917ghfzk0x3ijpvggbg")))) + "0695pjvp742qn629kxly4a9crbg6vakdx1ygnyshprjsz6xz2vnn")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -16672,14 +17702,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "15w5bmcl7h3fz6qhdqz4qc3qkg3pxcmzapg4mnnckzmyg8kh0i4l")))) + "0hrhfgv0b9ycw2vmzkpmrv9m9jvvq1n6asnxnrgvzlz81xak84ic")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -16715,14 +17745,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.32.0") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "1741raw1834093y5zhgx9jywfgz0wl0idlkynvab2c8vi40kc9a8")))) + "1h5pmd38b9zpbz1nngmk1s0cag4z0vx93yi2n7r85nca9z02cxad")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -16768,14 +17798,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1qyvwhmdv27xsyljyzyh52pn6x0wqx8rslvr2j7vqcjyywv270x6")))) + "1n17bpzj95hkljvgqpyv92jm4bk1d3j3mdg7106pb3dffvwv52sk")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -16805,14 +17835,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1cq5ixaxag5r6nvl73c8bznxkdjhxw1r7qx90ml7qm4jr7wyi173")))) + "1k3j1cbapzqk0qr3v4gijskp487xyz2n4lv4kia9y5pmplddxp7v")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -16847,14 +17877,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "19sl75168zv6qqmgsfnhcyw1z0lp0phmky40lsl6bbmy4k2hfw38")))) + "1j3wkqvha6pzd6d3wm2q4lihn8p9ycw0wmddjqpnqvglb1x7c0f8")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -16882,14 +17912,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1vjbk1vpqjxy9wv2a6sc32yyk0bhkbvdx9hl3vs5yjifwdswh2pw")))) + "16nkxnbsmr0y6km794x2iwbkyrkf0svg6ln3qkqnw0a47a3cbm65")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -16923,14 +17953,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc")))) + "0bhq8q3dch09r3digf3snfvhyj6w7j1qqw8gl28b29in8azg6v4d")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -16946,16 +17976,88 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flames + (package + (name "r-flames") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FLAMES" version)) + (sha256 + (base32 "0937zag0h4bvpapld267s5gz36h8zgjrgvbng9m7czdd8w6064ns")))) + (properties `((upstream-name . "FLAMES"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'fix-build-system + (lambda _ + ;; One target uses & instead of &&, which leads to a command + ;; being run despite the check failing. + (substitute* "src/Makevars" + ((" & ") " && "))))))) + (propagated-inputs + (list r-bambu + r-basilisk + r-biocgenerics + r-biostrings + r-circlize + r-complexheatmap + r-cowplot + r-dplyr + r-dropletutils + r-future + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-gridextra + r-igraph + r-jsonlite + r-magrittr + r-matrix + r-multiassayexperiment + r-rcolorbrewer + r-rcpp + r-reticulate + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-tidyr + r-withr + r-zlibbioc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/OliverVoogd/FLAMES") + (synopsis + "Full Length Analysis of Mutations and Splicing in long read RNA-seq data") + (description + "This is a package for semi-supervised isoform detection and annotation +from both bulk and single-cell long read RNA-seq data. Flames provides +automated pipelines for analysing isoforms, as well as intermediate functions +for manual execution.") + (license license:gpl2+))) + (define-public r-flowai (package (name "r-flowai") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowAI" version)) (sha256 (base32 - "0ydy98qsiqpw0b6fvmlv09kza94qjcl40ma9pknzgbq21ac4z25g")))) + "1bi13f8q7267lai71sl640w9zgd5a1iln5r4ri2dcskkwb2qxzkz")))) (properties `((upstream-name . "flowAI"))) (build-system r-build-system) (propagated-inputs @@ -17015,14 +18117,14 @@ the quality control enables the detection and removal of anomalies.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "0ig6xfhd70my5j4xrdy8srg1wi8nb3kcxlrld9py47psrq9vdadm")))) + "11xcz9b4mg3inz8c8f2vckgai67s740qjyynjim4ahf9zd0j7rxs")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -17078,19 +18180,23 @@ datasets, which increases the analytical flexibility and the statistical power of the analyses while minimizing technical noise.") (license license:expat)))) +;; This package bundles a version of Boost. We cannot use the latest version +;; of Boost here, as we also need to make sure that the BH (r-bh) package is +;; compatible with whatever this package bundles. (define-public r-cytolib (package (name "r-cytolib") - (version "2.12.1") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0mfv259k92vz0g7zv8zir2av2nlmx6na1f6q9zyj24s18m7mrkqz")))) + "1kagik93ddcl3m1i2bqzzlh18lbxywfn3pxmp47p45kayzxzldrf")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) + (inputs (list openblas protobuf zlib)) (native-inputs (list r-knitr)) (propagated-inputs @@ -17105,14 +18211,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.12.2") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1z3xsp1ymvdjhwcj5mkhl1d586rlr5i8vji9y5gs595w3naa4r0h")))) + "11aic1nzlw0gdpcpmky5jzljxgxcrimi29f0zl3yjvgb48qa88bd")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -17137,14 +18243,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "18lp1pickpd68fl7a4nidyvyh4yf53gbgn2f2yxaxfp2mk3mj88w")))) + "06n35c5fdkd3l8d5q8a23yslanirwhbf07b4f0zmf9a43zi642bv")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -17160,14 +18266,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0nrj4g02kx763wb70fzvhidmzp82gr1g3fp1aa1bv34cj4lnp47q")))) + "0z9vgd8v69iq8gv23iiaxrk77j2aq8y2n5k8x9jmxphbm0cm19a0")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -17190,14 +18296,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1hgw8g0b62k2lyswp3m81qczzwsyid7zdrnyjvl9388k29w2105s")))) + "13zc5952drl187fl07v1nh6gv0g6ba11vxpxl4ghvavnknvi5phd")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -17227,14 +18333,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67")))) + "1hn021p2220a47qzlya8qabc9xgmxk9gcs505m7wx6gx6ysdn418")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -17258,14 +18364,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.38.0") + (version "3.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1gmkmx6gzx4w39ijcad3lx2xnr2b833mhs8gcmc6k21k57aznzs2")))) + "1xg0hdxh0c1c1wc6d8gcynq8168hi61c3gjdf1223qvqwc39nsby")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -17292,14 +18398,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.12.1") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "097nxjijblqyz6nbpal7292qfijmk7x8dbx7plryr132xbaw5hdm")))) + "1i1a4ikfdyrrn0r53y1aipfm9dzzn6yzp5w651hvd6zav77cdh6q")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -17321,14 +18427,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.12.2") + (version "4.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1g1hym2anysgy7v46fnnxyzac3wzi1713vlih2gqzi23k8r2xx26")))) + "0sbixbq99kmhh0ppdid1hqhb75yxb6gsm5pdz75y67i3pgwrv1sj")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -17368,19 +18474,20 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.12.0") + (version "4.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "13mdpdndalm0d6azjancw0xcbdc674ivkj8kp6ccfpdd7gydhr4j")))) + "1f7qawn9wb8221npnmmygmvi4w1rq5lb74j3vmfzcak5kyga5xck")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics + r-clue r-cluster r-corpcor r-fda @@ -17406,14 +18513,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "0z0p09mkap1jqlq1x33i2ik87pbhwq85xgqyfsx4r360nhv06pna")))) + "12b4a65zgswzddkfdyl4j06qp7w9lkxv4h05m4z8hfff8c9x5bls")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -17442,14 +18549,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf")))) + "0wq9ganas6l2jw8bnajr7vwli35kykpgv2lca4qh79nfgxlicff9")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -17487,14 +18594,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "13y0ny61skj14mfhjwpa5zmflzdqxy2vf6gd4m9358g4wxfbhkv0")))) + "170xz3b4kfsxpqirfz9vk4j8dkdmz4qd0a1nm3yaya1rddpg9m3l")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -17523,14 +18630,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.24.0") + (version "6.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0dqndpmi56g772sra49vdrkjs4m9h2gzimwv3bwmw2l0krh2ax8s")))) + "0ifi89s611kblncnpvsrbl6sq2zi36binz63njrhya9wkyaxj6pc")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -17538,8 +18645,8 @@ self-organizing map clustering and minimal spanning trees.") r-corpcor r-dplyr r-ellipse - r-ggrepel r-ggplot2 + r-ggrepel r-gridextra r-igraph r-lattice @@ -17569,18 +18676,19 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p")))) + "1b3c1wg5xnhh4bdcjls26j6nsp0vx1g5y3grqv7x4ds01vmh3q2w")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs (list r-beanplot + r-collapse r-dosnow r-dplyr r-fnn @@ -17657,14 +18765,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s")))) + "1mcpx785ag0jcsh08df34hx3wp55zd1vggnl3fflkinb78178n38")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -17703,14 +18811,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "12zdygnwqjla99wzvvxzcmiwmh4v0rmnx4yix02gbj8xl4bxmm51")))) + "19vn31w74r45pq5m9pn5db1sz1qg757mghzzs933cdssnqf4m6y5")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -17770,14 +18878,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "0gagfm7v5bnnfj1zy6zf4cg91bj8nvv4vm38f3a1s4q2xc8pcvfj")))) + "098fbrszph5cnh4n9zjhj92sg1bi6h6k57wm2vlaqkq0nab63r63")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -17905,14 +19013,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1q4wi3k95c8vsyfx6359p2p29ascjg1cxmpp9bf99ixbjs71rd33")))) + "0bsid8qhcqgalqghr2b2592pzm4viyi7wq8h5dmhrrl7gky8l60k")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -17929,14 +19037,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0fq59bwc5i8zdw0v0jr5j5lm4hk6p7b88i2xndsgj4fq65yr50g1")))) + "12msc6skvcx4ajk20l71k32rj8lsiafjxwcsrd51kyy5x2yj2v4m")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -17951,14 +19059,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0qslh2xhhyaf0nsgcqav6qgh05n8kp0s6p1zggc02iid30i1ibrj")))) + "1ra21qzni9cny52ag9zxi46vb9grabyqjyk01dqqp3r9i0b4999l")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -17989,14 +19097,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7")) + "03qgiww523kijrkciln3fw3djn20rnvwz2j0i3p518h6fbl7vlpm")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -18047,14 +19155,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1l1ym89qqbq6qx07bm2p8gcl5zd9xh0nbw10fb7s0pfbrkj8xy64")))) + "1j80f7k39p23s6fym3nia73g8d1v44hdiv73igcq6fnsllxg40hr")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -18077,18 +19185,18 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "1sspl03m2hf6s5rw6nfqrycb236nvcgygql6apdlg3cjnikf090j")))) + "18pdpi855y1hhka96xc5886nqffjn1jhz9jr9p305iikdrsvmjp1")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs - (list r-biostrings r-genomicranges r-rhtslib)) + (list r-biostrings r-genomicranges r-rhtslib r-zlibbioc)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description @@ -18101,14 +19209,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1knzla5d8n22121a9licrjh2rxrmh05304a9d4bs2f1r7aiwhgnh")))) + "0w28b3ma8r8rshijdm5jj1z64v91my7hcvw18r9pdwjprh05bw0g")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -18124,14 +19232,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "0491x3m0015g83m6a7pkc4783768clgykhlcmd2xr6cgrhih10g2")))) + "1y2bk1kla0l72xgdam2l9c0k7584ckdqscqnc184cxvqm6fb335j")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -18171,13 +19279,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-tilingarray (package (name "r-tilingarray") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 - "0wj3wb4x9s0v189p20rlwghsx82x314yyhhsnfmrl266qb1ambrn")))) + "01j4wj0mdfrlyhp2alf1xfy78f17x43w9i0wb41ljw6pm313np58")))) (properties `((upstream-name . "tilingArray"))) (build-system r-build-system) (propagated-inputs @@ -18253,14 +19361,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0v0shsv0s9fzakdb4p84jfc4z57ryan27r1dkbvb3v25kjrhd8fi")))) + "01czx88dzqm8qv44kyy1n7b999wgfklxzgvmjh10chf677phnzsr")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -18297,76 +19405,17 @@ model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.") (license license:artistic2.0))) -(define-public r-genomegraphs - (package - (name "r-genomegraphs") - (version "1.46.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GenomeGraphs" version)) - (sha256 - (base32 - "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) - (properties `((upstream-name . "GenomeGraphs"))) - (build-system r-build-system) - (propagated-inputs - (list r-biomart)) - (home-page "https://bioconductor.org/packages/GenomeGraphs/") - (synopsis "Plotting genomic information from Ensembl") - (description - "Genomic data analyses requires integrated visualization of known genomic -information and new experimental data. GenomeGraphs uses the biomaRt package -to perform live annotation queries to Ensembl and translates this to e.g. -gene/transcript structures in viewports of the grid graphics package. This -results in genomic information plotted together with your data. Another -strength of GenomeGraphs is to plot different data types such as array CGH, -gene expression, sequencing and other data, together in one plot using the -same genome coordinate system.") - (license license:artistic2.0))) - -(define-public r-wavetiling - (package - (name "r-wavetiling") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "waveTiling" version)) - (sha256 - (base32 - "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) - (properties `((upstream-name . "waveTiling"))) - (build-system r-build-system) - (propagated-inputs - (list r-affy - r-biobase - r-biostrings - r-genomegraphs - r-genomicranges - r-iranges - r-oligo - r-oligoclasses - r-preprocesscore - r-waveslim)) - (home-page "https://r-forge.r-project.org/projects/wavetiling/") - (synopsis "Wavelet-based models for tiling array transcriptome analysis") - (description - "This package is designed to conduct transcriptome analysis for tiling -arrays based on fast wavelet-based functional models.") - (license license:gpl2+))) - (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.30.2") + (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "17jssd327l0miw52iadag2dbk8w4mhv2vwjpzdw89p8gww47bmbv")))) + "0cmcg39a5939y517vhvwanqh1fwzyx6pbq47nc5cpswf7pn9cv5x")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -18374,8 +19423,8 @@ arrays based on fast wavelet-based functional models.") (list r-aod r-biobase r-biocparallel - r-doparallel - r-foreach + r-corpcor + r-fancova r-ggplot2 r-gplots r-iterators @@ -18384,8 +19433,8 @@ arrays based on fast wavelet-based functional models.") r-lmertest r-mass r-matrix + r-matrixstats r-pbkrtest - r-progress r-rdpack r-remacor r-reshape2 @@ -18408,14 +19457,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "12p0jb9bpz4x612vwj77d6l5h8rihfkzmhp8qy1gvv2zmn2a54jf")))) + "14cff36ikbqhd5xizihpxzsv9jimcpbgnd381jd154pgi60bil0m")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -18438,13 +19487,13 @@ features (e.g. genes, microRNAs).") (define-public r-ucell (package (name "r-ucell") - (version "2.4.0") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "UCell" version)) (sha256 (base32 - "01qcwmiqri4xvwr3j4k1g062rfj6bbc0bvh0ifq1jq2xrm1azw9y")))) + "00v4b91f7y3zyndbl4wlfay8wljnqypfc05vrw15yr62d9smd35d")))) (properties `((upstream-name . "UCell"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors @@ -18469,14 +19518,14 @@ directly interact with SingleCellExperiment and Seurat objects.") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1gza678sd5m2rbki0l5hniki6gmds2cljkmywmk5v5m9swh9azq7")))) + "0v3jpnm3nq66xvckmc8447xl7wngfhhiwq6vjx54wgc6f586vmgd")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -18493,14 +19542,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0v1085dl16a3494f1fxc9rk1ffz3si89mdwbmnnczyhj5p13pfx8")))) + "0wy7zplypjiqv4wjq0l30xb5xj63fxb7z2wmmfrmzfkbgbm0xyha")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -18542,13 +19591,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "158v25ivbmsh54ywb5spfsd1nrmvfq83s8fkp14i7q5ckr2kvjhm")))) + "0ll0lksz6nzfj5ivmyrp5w24bhfl083amjpr0m8qlzpdw6k3wi98")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -18571,13 +19620,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "0k8fbwhh1w0b0zy5qgixmcnwxi3v78f1bjmjg1yx6paniwk58bzn")))) + "1qckqdil1cq8lbrj9di96w9934r1fp48xpmfdwp4f2vw9pjadi1q")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -18595,13 +19644,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "1z6j4wy355pljn9wf12zzq4zqrhaik0i2phy7jg89jsys7n2mlxy")))) + "0cy1f4ki4j7yxc9cws5s17ljd4ac0yxhijms0pm31im81qz2djax")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -18622,13 +19671,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "088dq6mc9m1bx0dprcz8cdpfp447lnxq7420r139mhcik0z21vky")))) + "1rqyjj4lgqxs372qx8p3qx2napww0djh4jz8hzgv86x9r202kk9p")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -18687,14 +19736,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79")))) + "0mgvxpqaq0jncr1kzmwhqkv3pajx2fz6vwhv5arw7fgla6w09p9h")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) @@ -18748,14 +19797,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "1g6k3ryj8dz17asa4imnrk77z4dk9an5ssrqr17r0g797d5f4qjm")))) + "0v85i0lwmxq5yq9ygfzljgy8fsflqq1p53rq8aasnndd6gsm8ld2")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -18784,14 +19833,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "0w60h1jr9kwvgg5d6bcrq4gl1aa1v6xrn43ymsc2312019psrrjy")))) + "1m289q9bs7i7d15g5mzdmzw7yppnqspr8illkya8kxlv1i2sify1")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -18810,14 +19859,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1q7dsvj6nvczs76jcxyy77298vgk4zk083bldmbbgnwparrgjii9")))) + "10inwxl1cmkdp8037wcwkj5wzxsrrcysxfbqhnkh7pzhzvwnzz9h")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -18832,14 +19881,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "05lwz2pw2vnhmlhp5vv9j45jrc5ssdw4lx6mkxnsvds8zl3y9294")))) + "056zqlql39q44snvx5nzc5snrihpr1kj3jdbpbb401hxi9r64f4r")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -18861,14 +19910,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "0mgg1qfvxgyjk6fw4x0cv486vrsgf1kbqr6nqhgxj6lk8w6909fm")))) + "0pvj0qgc6hd02g9ppfc610gvfn412rw69rxh43y4dr3n894kdm2i")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -18887,13 +19936,13 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hybridmtest (package (name "r-hybridmtest") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HybridMTest" version)) (sha256 - (base32 "19pycad35hc7ylnsz75bv029y1r6j9xvrbhzk4i64i7jn8gi7ngh")))) + (base32 "1jkihcad453d7jqb78fl03yfqz169jz75c40y53569ndp2j4rg71")))) (properties `((upstream-name . "HybridMTest"))) (build-system r-build-system) (propagated-inputs @@ -18918,14 +19967,14 @@ then the law of total EBPs.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "13f3m8m6i99hzm94hriry645jcn0a1ki8z8wmn3mkasdi6bzx20h")))) + "16bjjfzcndjfqsywzw2cn551fgqlnll2gi975w0qqxhkh3jssgmi")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -18940,14 +19989,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0vhfvmv6b3kab6a8hy2y9zwxgzwb5vliaaxhlrgz8i4pvvq5nhqb")))) + "1lgfpw9f7095lgk46gdpxq3z52c24xw4ajl7yid3pcgw19bfcgk5")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -18962,14 +20011,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "03pd4a3l912zdfk35flagikqimp01wp76nslid32l43d7yg9p57w")))) + "1pdsxkh9fkgn80f7p21902pb6xp2qafq10p29ifb55qwz8gma2ff")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -19069,13 +20118,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemmineob (package (name "r-chemmineob") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineOB" version)) (sha256 - (base32 "0l44d6l078k1w5nf7i4sarah1zn30zqjmcj9qpy4hhg97dfy45ci")))) + (base32 "0mfajzwzldmra6g5kni5yw7m2n719456p1vd3hxx2r7l1phdjixi")))) (properties `((upstream-name . "ChemmineOB"))) (build-system r-build-system) (arguments @@ -19110,14 +20159,14 @@ add-on package rather than used directly.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1m4vgq3z0kya7kbncawr9csvbwnh74mh012w7g2ialwd3nwdf91x")))) + "1328mwmghflrvir1i3crlq8q36wq60x2an11saabg63hnx4paa81")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -19153,13 +20202,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp")))) + (base32 "17il9mi1iagl474ia1lz0ajx1wq67jw5famkr1fmjlis8ymw8hnd")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -19182,14 +20231,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0ilwniyrp3m8mi1vmggd17f9g6wdw7a78l2db190w29alzpbfmp6")))) + "1mm1nzdz9cl8mf33yiyaspqkx4sbqhhs6m9jfgl42fhscrhaxfsi")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -19217,14 +20266,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "0kb6ylq94vywfky0mcrva109darcv361sqvwb19qn92p8vh5199l")))) + "1ivclipy2igf8ax7f0pqrcqflcm7h0a8ny6nfa0200vp99an8ymf")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -19246,14 +20295,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "1fhjkgl6567qchi5sfdqnznalm1l7c7pabz8jc9d7ib9x4g922q5")))) + "1h8j10jx02zsxs6rzids3gy4xchdhgzkifa5grrfbn8faf9ycy2n")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -19270,14 +20319,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn")))) + "0kflwlmyckyivr8xh7fsmpl7jfkq5kavwpkswmvdfqckbd0n9xsc")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -19303,14 +20352,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1k50br4hpkrwv1lnn0wp1c7kj32vk0gg19aivmw5d6brjdd39c1f")))) + "1m8dy1lmx9m8p5jjk0i7yllb4pvq77kynszk1nz8cc1niz6xs47q")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -19325,13 +20374,13 @@ microarray data.") (define-public r-biocbaseutils (package (name "r-biocbaseutils") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocBaseUtils" version)) (sha256 (base32 - "143fmjbi8spaj3njvc1xvsjszfxs7bv3vxik8pisw5y8lqzx7hqm")))) + "189jz8krhv0vdnk47m3cmy95zfg3l328w6dbhg6djvlkca17i275")))) (properties `((upstream-name . "BiocBaseUtils"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -19369,20 +20418,22 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "0a0fnmqln13iglnw8smbbr4k7hdvacipxa04zhqylygpsq1246bc")))) + "11d67dfwxc34n7yzpz58ficjk7sxnbxrajhnqlcxvsifgmybkb4d")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - (list r-biocfilecache + (list r-biocbaseutils + r-biocfilecache r-biocmanager r-biocviews + r-callr r-codetools r-graph r-httr @@ -19399,14 +20450,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "0fnncmi82qb9lkg1zfyps7n3nrw1s3wcqbixh420w53hmdyryryl")))) + "1yy0bwvfa5b531jvmbiwrd4xg8cdvrgwr8l6bxasrh6yrbv8drml")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -19421,13 +20472,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "11v3gzy88fai0rhdymvj9k74g7hjc6n9fihfrrnw0qfr447z1d61")))) + "17pkdi3vn62pw1nzmgz0i45czynqjchq078ij8v1xvflg6lf7flw")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -19445,13 +20496,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.68.2") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1icnaj1ifndym7nl1yafzd0y0fxyhzjyb4qzqpcnsqhh4yi3pnm5")))) + "0fpka47shrxcbc1k057f5zv79406daic0y34v8p5lsvxbgzh0m8b")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -19474,14 +20525,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4")))) + "1prl24sg5l142155z3iaxrvig2wv2xqajq02nj30jjjih4p4936w")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -19504,17 +20555,45 @@ and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) +(define-public r-experimenthubdata + (package + (name "r-experimenthubdata") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ExperimentHubData" version)) + (sha256 + (base32 "0msg3wpz1ppvwc4dsm9bz9h4y4hz67xr1xwp4vv4100sg0i5v9jn")))) + (properties `((upstream-name . "ExperimentHubData"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationhubdata + r-biocgenerics + r-biocmanager + r-curl + r-dbi + r-experimenthub + r-httr + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ExperimentHubData") + (synopsis "Add resources to ExperimentHub") + (description + "This package provides functions to add metadata to @code{ExperimentHub} +db and resource files to AWS S3 buckets.") + (license license:artistic2.0))) + (define-public r-grohmm (package (name "r-grohmm") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1zg30cb4s97zdv6c0f53ix6a97aan5w3lx698sa4cqvi4hbz8f35")))) + "15ibdbpj7vqypxfnp2w06w9lync11z3azzss6s97xhadkgsbw4vq")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -19534,14 +20613,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "00xgca1q9ai5x730bvx73f25lpwkr3dn2sia3msa49fpl4nrzr20")))) + "0dmhqymh800mljcpdf817nbyg20czp8y9bg13p3r4bfj6axxckch")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -19571,14 +20650,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "11135a4l0vn84qmpyclz052zy45s0m38av94604jqxgb51q9lwyf")))) + "1xymgfiv9abyaq5s7m683ml8a1ls9mqvbh9qjiz3jqbbpvmsm502")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -19617,14 +20696,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p")))) + "0710dl05hs590fimp3dhg5hzvk6s79i0kwk6w6sj59pcawx2l6il")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -19644,14 +20723,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "16d0sjkzagc0jxha28qxplg6iihwg2q05sig0s1291lm7kh5k9j8")) + "0swi6xiads31xcndc2cfzh0ivdl0wc88s83s1p1gxh51rgmgkb14")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" @@ -19758,14 +20837,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5")))) + "0sk4kmvl86xm85dqaf8gvii0qavyycyn2qp0v6dmfcjqai528v2x")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -19796,14 +20875,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1zvjj0hpqwdv7yifqwyb14166ppxw91d964gz4xclism5z5lvyln")))) + "0mh7lsiprshq56ns3b8pbv1j1mjcbdzqydvli0ynmvf5smn2j4m5")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -19829,14 +20908,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1mx4abv7p76qsa0yzj0b4d03xklx09im01bx02lwa1w527gdmfc3")))) + "0ngpysb89wag4wvcq83ddjxhy1zhl32b2fy2fg5laa4g8xfrqaxz")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -19851,14 +20930,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "07kl7s2zd7nkhg4hib2mr3w5lhqy780aw53yqsd7bfsjh53k8g95")))) + "18rzv4kldjmm2zvz9pzrpspig2hy6mcvb45hgmw49ba4jdcxh31s")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -19897,14 +20976,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0qq3fqzd973jlf6ibfww5yicnyz2qvs2b2mn35p77k2mp4d7qp52")))) + "09fvmfiavawfwbxaj1585l2n00fibx9z3r17dv06hc6b40a1sa12")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -19924,8 +21003,8 @@ dimensional mass cytometry data.") r-org-hs-eg-db r-progress r-rcolorbrewer - r-rcurl r-rcpp + r-rcurl r-rjson r-s4vectors r-shiny @@ -19943,14 +21022,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "158brq3w5h735s9yq93xx0y4p79yhgz72rpy0cyk4fjia5yaij5c")))) + "0q6npc5pglmhzm9270pi11kbp5wg3ncvflp4rhv3w778qza2zlk1")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -19976,14 +21055,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1aq4iwk1cp96jzldhx7d4q7i77zbdg8nzkzh12g29yhwzj39nl3q")))) + "0fz66bchf41jzgabs1s8drpi3f7g27lid5g50lxwh6ph3i02cpaw")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -20025,14 +21104,14 @@ plot them, and perform logrank or Wilcoxon type tests.") (define-public r-fhtest (package (name "r-fhtest") - (version "1.5") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "FHtest" version)) (sha256 (base32 - "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q")))) + "0x7lr88w0b09ng7nps490kgj8aqdjzmp9skv9iwqgn871pnpydms")))) (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs @@ -20099,14 +21178,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.62.1") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0z37ag22j1wh80vwq1kyr99rvadj9ppkddapfqyql3vj5x44cf4d")))) + "15fy3vwnjx6rwrkhbwxyvdykkfdis8c0m18x6y7irvyij9lm6x1y")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -20120,13 +21199,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.0.6") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "011n4lyznlrya5l8d7m30x81k7h81wbp07b12s6a4s5sy9fzd5jb")))) + "0x420l98f6b10r3qrdjq5ijs2p0msdcg6d6aghr3yvj1f9g06h8y")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs @@ -20157,13 +21236,13 @@ array-like semantic. It also provides: (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.38.2") + (version "0.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0n1w451647pxii6qrrxbvdi9z6rqdwibczkbs7k7a9j33bv3nqv8")))) + "10lryil0psfyal0006rbhj0dbxyn8f7mpp11h758zc217cxsdnac")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -20187,14 +21266,14 @@ S4Vectors package itself.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.72-1") + (version "1.72-5") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1p3zsl5r6l5r6ylnrxmbxjpim5qgmncgdjcgn5j69rzk3rv85gqx")))) + "17g7lan1rpy6y4nmqksrf9ddp3gs58vdczfavgq1fp13zx1r2hq3")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -20206,10 +21285,10 @@ S4Vectors package itself.") r-go-db r-hmisc r-impute - r-rcpp - r-survival r-matrixstats - r-preprocesscore)) + r-preprocesscore + r-rcpp + r-survival)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -20225,14 +21304,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1dv1vk73achjz5b5zzw2d517nbjfrlj7gppd48pfhk1w0mvz3q61")))) + "03l6yr76inv4fivy10g0h2qafgywrcjnnhs694lwqz1y6r0gm1sy")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -20263,13 +21342,13 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.6.2") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0zsw4j6gk25303xpdwnkda2sq3mb4zb4p1mzwiyf7hdyf87zis05")))) + "04vl4cp0izghm7h4xk7x48lqkq0dpl47dkd068lva33jygwwpvcz")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) (propagated-inputs @@ -20299,13 +21378,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0mqrzh1rcwyqlhq9wxcy4gp47hsb70qrsissm9nj0cb9j6ihi407")))) + "0ygcq3xi55swsmysn539cr3m504rfb6zm30w747pa46r63dfjda7")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -20323,13 +21402,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "00csfr3yhbllwc8797xg49qb0djpvbpfi6mbnps284nlqy5vpdwh")))) + "16svq29fm9xl3rl9v6lyxf564manvp8ryxj1mbxc4pb360wmi780")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -20352,14 +21431,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1riwxxnbi4z0lf42psh3m3ivxlgmmlnqhgsih6911c754r6s39qg")))) + "0p52n96mydqszpq1ysmbh5xs4n4icqsd0gbxl5wpkcwvvhxliw8b")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -20384,14 +21463,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.22.1") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1007i2rzz86k04kswa4h53p8zzh52k31m9d8im6iw0n91inqbcj9")) + "0lb5dkzfnfvxwrk8s9vzfjp8ab1sbr7b22jnzg41hgmpysi7dswh")) (modules '((guix build utils))) (snippet '(begin @@ -20429,8 +21508,6 @@ block processing.") (substitute* "Makevars" (("@BUILD_HDF5@") "") (("@COPY_SZIP@") "") - (("@ZLIB_LIB@") "-lz") - (("@ZLIB_INCLUDE@") "") (("HDF5_CXX_LIB=.*") (string-append "HDF5_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) @@ -20447,14 +21524,18 @@ block processing.") (("HDF5_HL_CXX_LIB=.*") (string-append "HDF5_HL_CXX_LIB=" (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) + (("@ZLIB_LIB_PATH@") "-lz") + (("@ZLIB_INCLUDE_PATH@") "") + ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - (list hdf5-1.10 zlib)) + (list hdf5-1.10 r-biocstyle r-stringr zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr))) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown))) (home-page "https://bioconductor.org/packages/Rhdf5lib") (synopsis "HDF5 library as an R package") (description "This package provides C and C++ HDF5 libraries for use in R @@ -20464,17 +21545,17 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0ga9y9npl885jdx7gw5h6lh7fr0z5p7cvcwpz3hvwm4dy235j6gj")))) + "1yixv6vs1q2k4vx17bq4nar3g4v2076i5dq77gh63mlka46qr3g2")))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) + (list r-biocgenerics r-delayedarray r-matrix r-rcpp r-sparsearray)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/beachmat") @@ -20487,13 +21568,13 @@ matrices.") (define-public r-beadarray (package (name "r-beadarray") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beadarray" version)) (sha256 (base32 - "0rd41193rq6v4a97ibp0l2bz140nsv91plhn7iim8d8n9hgxqhjp")))) + "0qwka7549mlv2x80bjrzdsy4a6h35yxrhj2cxss9aigwsbjb7sjr")))) (properties `((upstream-name . "beadarray"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -20520,13 +21601,13 @@ quality assessment and low-level analysis are provided.") (define-public r-beadarraysnp (package (name "r-beadarraysnp") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beadarraySNP" version)) (sha256 - (base32 "1pymsm4j3wiyjvgsjb3vhjwdvhfmh91pxdhg4ihrj71pqpif3w9m")))) + (base32 "1vrizh7fpzv1w2gki0qxhphrfj1jj6m6bjsjsbw0b4n4invybzps")))) (properties `((upstream-name . "beadarraySNP"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-quantsmooth)) @@ -20540,13 +21621,13 @@ performs copy number calculations and reports.") (define-public r-beaddatapackr (package (name "r-beaddatapackr") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BeadDataPackR" version)) (sha256 (base32 - "0hm4brxg2rxazdcnhjiz6f4di2q8wssrrp35m79vm93sac9w42y3")))) + "0sfpdpw6qqffzb9skzx9w1ggcixc3wry9c6f2kwpsykbdsnk90xz")))) (properties `((upstream-name . "BeadDataPackR"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -20563,13 +21644,13 @@ decompression of raw bead-level data from the Illumina BeadArray platform.") (define-public r-cner (package (name "r-cner") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "04arfcr2ay71hyy0xsh6jzappmcnnzfr1nyj1l7dqhhhk81ksjfd")))) + (base32 "0kpz15l3yz26s2kskxk4093313c7vwi131y24wbpcdahicpqys2m")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -20611,14 +21692,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "136s96cmd1aq878xy9mqd4k46awywqpmm55lpvash8mv4gg02vg8")))) + "18msr889nygk1c3wsjxc9bv989zakkl9f1h2a6cnfy8rxhbxpvwq")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -20657,13 +21738,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1jvmqn33hxzscr8j7y9zw5sngglcy0zkl0386053lx5dl5s5iqyq")))) + (base32 "025wlqnx13ldzyrf72mrfj492d62i4xyjbhpmgavgld0jwfmr3ga")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs @@ -20686,14 +21767,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "0vqsxfbrxs25xr27vsr5syqjn6fwvn5dw0g76w4rdqk5d08p56ci")))) + "13kkg9xpyvgqpsaz5f96pd43i8a45jrbnzqmax793zkv4ai8p16j")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -20720,13 +21801,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "001133rfcwmf4p3dbif933y9i1mkr3krw38g646wj4ikycszwih4")))) + (base32 "1vy650625b9b2dgnkgh5h0kw5bkdvfin133091asf1nw4jgnn1vx")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -20767,14 +21848,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1v2px6gvr0wzj2cyml57hxj5ghynlvizkchbywd3kx05j1h2mckd")))) + "0q44n97mly1ldh52r0sb1jwhz8bn4n7sfw99qs5h4s44w9s0fry4")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -20795,13 +21876,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.2.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0dwlg86wkivsag5ffjk81nlq34lwl3kk065k9l6lak24ziq6c4ij")))) + (base32 "0zlv45diasff5ipxp99dddswclrzzdcmkqp278fm2cj7aibvb3sd")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -20827,14 +21908,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0225fk3ca540b9z3dd5q2zngxsa524nq7zrv1z5qnmr2knc0yxfb")))) + "090arfacfs09x7g60qxz4bj2gqb97y3kmhafywkgnrj7pz1z0qzq")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -20862,13 +21943,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0v6qaflv7b504yxxv6bmnlikg36bhfahgqxigpq6qcfrhqapmqck")))) + "06a4nxxsgmi435m06ir401w4fbrh0xdgh6mkv3i7vw001yrbrfcx")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -20877,13 +21958,12 @@ of other packages.") r-biocparallel r-biocsingular r-delayedarray - r-delayedmatrixstats - r-densvis r-ggbeeswarm r-ggplot2 - r-ggrepel r-ggrastr + r-ggrepel r-matrix + r-matrixgenerics r-pheatmap r-rcolorbrewer r-rcppml @@ -20907,14 +21987,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.28.2") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1la55s14frvsjp8ly02fbrkzvv7lzvcd7jc1axmwh494b9zy5jmd")))) + "02840dw467dqdg09abxlzps1l1xnzhinlmpmqgfsq70pzqf7jywk")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -20947,17 +22027,54 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) +(define-public r-sparsearray + (package + (name "r-sparsearray") + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SparseArray" version)) + (sha256 + (base32 "19cy1nmmi65fxh012ymgp1kg112yl1m0khcs4y034p5iwlfv7fp6")))) + (properties `((upstream-name . "SparseArray"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-iranges + r-matrix + r-matrixgenerics + r-matrixstats + r-s4arrays + r-s4vectors + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/SparseArray") + (synopsis + "Efficient in-memory representation of multidimensional sparse arrays") + (description + "The @code{SparseArray} package is an infrastructure package that +provides an array-like container for efficient in-memory representation of +multidimensional sparse data in R. The package defines the @code{SparseArray} +virtual class and two concrete subclasses: @code{COO_SparseArray} and +@code{SVT_SparseArray}. Each subclass uses its own internal representation of +the nonzero multidimensional data, the \"COO layout\" and the \"SVT layout\", +respectively. @code{SVT_SparseArray} objects mimic as much as possible the +behavior of ordinary matrix and array objects in base R. In particular, they +suppport most of the \"standard matrix and array API\" defined in base R and +in the @code{matrixStats} package from CRAN.") + (license license:artistic2.0))) + (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "00jalzg6yphi8ci4iid7x38jlsrvvdswrq7cqa7jybs26ayjldw1")))) + "0r2jxwha2xjp8iy7al85s5vib4xvl47gmlbbvvjj4wnz2gfzic9r")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -20975,18 +22092,17 @@ data in the column sparse format.") (define-public r-spatialexperiment (package (name "r-spatialexperiment") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SpatialExperiment" version)) (sha256 (base32 - "18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70")))) + "1s42jzq95f662h39zmbf06qmrrglbch8sgygpnwqblrjbrqgm7n4")))) (properties `((upstream-name . "SpatialExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache r-biocgenerics - r-dropletutils r-magick r-rjson r-s4vectors @@ -21007,14 +22123,14 @@ Visium platform.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.22.6") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0jaaqa2fm61dmsphm5y4rlwf2dm1l5rs0vpq0f5r35iyw2m12lh8")))) + "18r5rfx46lac0kaakha4gqs4pj8vb39z0908gpclmp3ajca4hzb1")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -21023,7 +22139,6 @@ Visium platform.") r-iranges r-matrix r-matrixgenerics - r-matrixstats r-s4vectors r-sparsematrixstats)) (native-inputs @@ -21043,14 +22158,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "055xzlq37d75ghfk87bxbsv4yifidnwxc3w2gp8mcqxwkxxhd70a")))) + "0l6rdkpg89pds3n5y4khvaifgbvm38n0vlpi15h97rnk8x461rsz")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -21072,13 +22187,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "0cb4b0mf5yh8amqwa3r0mbk2f3rgq40gdlkhifk50fxnqdy4fjsh")))) + (base32 "0vpsc7i6j2skn6wba178iy406yvd4p8xf3lq2qmm2inimxl983cs")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -21102,14 +22217,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "03hslg7k6khchf54gmlbkvwbkfn5ppz0wp7lh75gsnr0licsjkwx")))) + "0bn2jknvj2ag1yv67kjqr7gsq771rmqv3my9njjkwcc9nzrxzhbp")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -21135,14 +22250,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "108azzd6ibcgb1gqgcrz4shk3rdr3vfpzy0z6zknlsxwz7sbcnfi")))) + "0xxjkr3x654n61q2yda09cghvssyx4ml9g22gfzfhbzjp8j7pm2c")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -21158,14 +22273,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1y3nklhlib2l9smcl6slv1653vyg9ip29if286l59rjrdwh50cwa")))) + "0dif4yvm9hfrnamjph5xa9cbf41f2v8lbgyr88f11alwwbf0dg69")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -21187,14 +22302,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "0f6h0qngv7my83k402rydvi1pla695r5kxq02k1s5caxcsi1caza")))) + "0dfg9ib0imk8bmhycqrspnn8yvfdlchwvx39wgqxi5fb9zrppfz4")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -21211,7 +22326,6 @@ relevant, and the minimum expression of the most abundant condition.") r-ggrepel r-ggridges r-gridextra - r-magrittr r-matrix r-matrixstats r-nnls @@ -21250,14 +22364,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "14rgj8g9x248p2cc86aqn289qamsd91d6fnydi5d34q605ph73yj")))) + "0vapjfzhwlzxd049fsr00jd7lp48h9qwd95m2sqhqryqz1vsi7hz")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -21290,14 +22404,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0n7nghrrs7fp0b7jk2pfbkzl0lbv55xxk2xqnq2i77ps22ms0h9y")))) + "1chs58ifpwz4crcl5ymnb8ah3wf2jrn9lla3ljsywqiqn0r3i1am")))) (build-system r-build-system) (arguments `(#:phases @@ -21458,14 +22572,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.44.2") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0laismy8kklzkg81r5vf1194fbhp2hw952g6jc3zvn2z5y2d4524")))) + "0an8hd2g2hp3p1vfsmxq77fm71xlf5g73j4w5mcy28x1aj073zxf")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -21507,14 +22621,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "1i64bk0ac2v0w5yjxdhnbjh05l6n9fi7gxap0zp73wxj7kl75wkd")))) + "028n8v1pgkr1q5s9wslql8ayk1cbx6a9a2rjka9pdwz6rq1iyagy")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -21541,13 +22655,13 @@ EMBL-EBI GWAS catalog.") (define-public r-gwastools (package (name "r-gwastools") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GWASTools" version)) (sha256 (base32 - "1g86xg2d9wi6xijhc89zxhbw190aviw9nkwvbwgz85jf71wf34hv")))) + "1rjgdcw65zmmg5dy9mdaz720nvqk03bfsfvkdsa1wwhvlnxmscp8")))) (properties `((upstream-name . "GWASTools"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -21562,6 +22676,7 @@ EMBL-EBI GWAS catalog.") r-rsqlite r-sandwich r-survival)) + (native-inputs (list r-knitr)) (home-page "https://github.com/smgogarten/GWASTools") (synopsis "Tools for Genome Wide Association Studies") (description @@ -21572,13 +22687,13 @@ annotation, and functions for GWAS data cleaning and analysis.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl")))) + (base32 "0i9iqr87mqih0rkbjx3wa383x4yfyzpcb0b0xzairbqgygvcq4kl")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -21596,14 +22711,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "18gqmwwi1i4gndqljy809n5zzx38agawxxwhlknpas6k2iskd1xq")))) + "1caxzc99kga2c90m2ydmnvcd8lfp0igmmickpl0ikrhwjlbfnc0p")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -21652,14 +22767,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "3.0.2") + (version "3.0.4") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh")))) + "1qqsm6ldbf6rnzvspcnv87l4mkxccg4divzf6nj7j92jnhyadqia")))) (build-system r-build-system) (inputs (list gsl)) @@ -21718,13 +22833,13 @@ other functional sequencing data.") (define-public r-parody (package (name "r-parody") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "parody" version)) (sha256 - (base32 "0n2pmpnpwh16hb58v821xn42jm4a7wjsdf6sqxapjjw9w432mjac")))) + (base32 "05mhbkhyh92bwmx37fpviprr9i4z0i6g24l71zk17gq0f8hwb4jj")))) (properties `((upstream-name . "parody"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -21739,13 +22854,13 @@ methods based on resistant statistics.") (define-public r-pathview (package (name "r-pathview") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "0mld7vys6s5k8snk1gniph9wkw3726vsx430nhyyr76fp4ps2mks")))) + (base32 "17kl7yvpjhsb52kz1pw3jnk6s480lnpvvh9rragndixsl8bkmqmc")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -21773,13 +22888,13 @@ large-scale and fully automated analysis.") (define-public r-snapcgh (package (name "r-snapcgh") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snapCGH" version)) (sha256 (base32 - "0yz5q7w3lqv8ac6a764xlbm4hq3ncnngqng879qbpmzhgb4r155g")))) + "0knjspxzc3z5dhx0a6kx9rkic85w65l84vy552x5bv8jzxkcwrsj")))) (properties `((upstream-name . "snapCGH"))) (build-system r-build-system) (propagated-inputs @@ -21801,13 +22916,13 @@ segmented data for individual and multiple arrays.") (define-public r-snprelate (package (name "r-snprelate") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPRelate" version)) (sha256 (base32 - "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh")))) + "0jw9ziz0a472mnnvmqwas5w646xfgx8dn1bdpwz8c99m663d8ayp")))) (properties `((upstream-name . "SNPRelate"))) (build-system r-build-system) (propagated-inputs (list r-gdsfmt)) @@ -21836,14 +22951,14 @@ whole-genome and whole-exome variant data.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1v2j2943apphs8i68ap9c8sxd4j5a04qda5scq4dqqkzqd0c5b6i")))) + "0a4kyv93ljv7n62ghx66l81q6sw24llr0998nsalidyws1wldbyr")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -21860,14 +22975,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1qrcmydk080m1rzwbzx2km4vpbahnq5y73mrnpgjjjrxbndz9xz9")))) + "1yykcqxp8y7by4jgh6dfl25m0pnghj36qy21990n2sdfv1kpg2x6")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -21898,14 +23013,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "1v1yw90waq0ccj6pxdipipy5bnk0k762m5kadl4h3jgpcrkf2fvc")))) + "09i6j8dcmzvd9gh9629523hw0hbng18jdqw5gf1r31ck8m8wwmnc")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -21951,14 +23066,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx")))) + "1r3qz6y97zhp7swcv2ls1h6cz0l66y5ap00wx9wlqxv14sljd135")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -21985,14 +23100,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "1zzhgfnrr3r5ismbbj9jcqss8mr8ll6p4d3z026ya2khb0i7clc7")))) + "0g9d4q6vh2ys1la15fqgbc4ckfbjbzzaqa49x9liqrhpnrp59vc3")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -22018,14 +23133,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "1sdw69dhrzkcpc7flvp1gkixvpsbrckyg756rlm17hjjwfxlz5lb")))) + "1a8jmlx17qcx9qzcaxbnlk6qji6hqxcnzmr8zvar9jrfhx0cv9x1")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -22052,14 +23167,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.16.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "0j83scxpq51bhxwfps7chcawzsqrd7pk7x2jg29zj4zbp1jbrnl0")))) + "1ipypkyfqx6mahiwl0gzdsi7z9j9cm5rgfw4ybgh6blfq8kg9qyk")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -22088,14 +23203,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1s6v17bavidlfy6habi4bv6lmwkrx8c5was1zcq0kb05qdvpn4ph")))) + "1ahip21wihwg9yhq0ya1cyzd2cq423hz9pd6iql6y3yhld4j5rnn")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -22122,14 +23237,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0cbhlxh0w736695niyjd59fcvplna2f2x2av9k0sd1r3dy6lrcd4")))) + "18p5r67ppkw8wxxkrj76q68ljlhdbhar5hc89ffdsgr3zzdyk875")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -22146,14 +23261,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.58.0") + (version "3.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "04ll8nqhmyj2v12n2xskia8dh5px8mzj8fbyw1pzahk9vp085gkr")))) + "17v2x7cyw74h0zfsz33pyl1kqk976pdzw7mrgprz9l7w5120niw5")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -22168,14 +23283,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1bn7h8jwmmgqzp0s3xdbsicm8pxmrgvnxmjnjs10d1rvp8znzjnn")))) + "1k61aka780xmf1vhqm6zvzjr2626hv71f8gp1s81az939crxlrqd")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -22193,14 +23308,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "1vccq28734s7zk7pc7i9zq4rzbi373xqqvgkzamjpii36phkdmlw")))) + "191b8qhldxvsw09l2c0ffc1ldmx0mqxgsx6m074f28l01d3c1d9q")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -22214,17 +23329,133 @@ within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.") (license license:gpl3))) +(define-public r-basic4cseq + (package + (name "r-basic4cseq") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Basic4Cseq" version)) + (sha256 + (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4")))) + (properties `((upstream-name . "Basic4Cseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-bsgenome-ecoli-ncbi-20080805 + r-catools + r-genomicalignments + r-genomicranges + r-rcircos)) + (home-page "https://bioconductor.org/packages/Basic4Cseq") + (synopsis "Analyzing 4C-seq data") + (description + "Basic4Cseq is an R package for basic filtering, analysis and subsequent +visualization of @acronym{4C-seq, circular chromosome conformation capture +sequencing} data. Virtual fragment libraries can be created for any BSGenome +package, and filter functions for both reads and fragments and basic quality +controls are included. Fragment data in the vicinity of the experiment's +viewpoint can be visualized as a coverage plot based on a running median +approach and a multi-scale contact profile.") + (license license:lgpl3))) + +(define-public r-basics + (package + (name "r-basics") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BASiCS" version)) + (sha256 + (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8")))) + (properties `((upstream-name . "BASiCS"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biobase + r-biocgenerics + r-biocparallel + r-coda + r-cowplot + r-ggextra + r-ggplot2 + r-hexbin + r-mass + r-matrix + r-matrixstats + r-posterior + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/catavallejos/BASiCS") + (synopsis "Bayesian analysis of single-cell sequencing data") + (description + "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an +integrated Bayesian hierarchical model to perform statistical analyses of +single-cell RNA sequencing datasets in the context of supervised experiments +(where the groups of cells of interest are known a priori. BASiCS performs +built-in data normalisation (global scaling) and technical noise quantification +(based on spike-in genes). BASiCS provides an intuitive detection criterion +for highly (or lowly) variable genes within a single group of cells. +Additionally, BASiCS can compare gene expression patterns between two or more +pre-specified groups of cells.") + (license license:gpl3))) + +(define-public r-basicstarrseq + (package + (name "r-basicstarrseq") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BasicSTARRseq" version)) + (sha256 + (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa")))) + (properties `((upstream-name . "BasicSTARRseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BasicSTARRseq") + (synopsis "Basic peak calling on STARR-seq data") + (description + "This package implements a method that aims to identify enhancers on +large scale. The STARR-seq data consists of two sequencing datasets of the +same targets in a specifc genome. The input sequences show which regions +where tested for enhancers. Significant enriched peaks i.e. a lot more +sequences in one region than in the input where enhancers in the genomic DNA +are, can be identified. So the approach pursued is to call peak every region +in which there is a lot more +(significant in a binomial model) STARR-seq signal than input signal and +propose an enhancer at that very same position. Enhancers then are called +weak or strong dependent of there degree of enrichment in comparison to +input.") + (license license:lgpl3))) + (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.12.1") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0g5apvna9wzjlm7g9hdafy44nrg5rp3qh4anwpgwwp2vr0vxn37k")))) + "19m4h90rkk6mizllkih2xmxag8nb45qss3vydkkyj62s5zjhfh27")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -22241,14 +23472,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.12.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "0bg6jfl12jsmhgby7x7g2vfmi61rx0jdksi97hb0zajgh1nvhirh")))) + "0fi3211p7fzab0bw2zqkc7gnqzpi24sf8655wghaw3yg9g39ksdg")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -22264,17 +23495,177 @@ Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.") (license license:gpl3))) +(define-public r-bayesknockdown + (package + (name "r-bayesknockdown") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesKnockdown" version)) + (sha256 + (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8")))) + (properties `((upstream-name . "BayesKnockdown"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/BayesKnockdown") + (synopsis "Posterior probabilities for edges from knockdown data") + (description + "This package provides a simple, fast Bayesian method for computing +posterior probabilities for relationships between a single predictor variable +and multiple potential outcome variables, incorporating prior probabilities of +relationships. In the context of knockdown experiments, the predictor +variable is the knocked-down gene, while the other genes are potential +targets. It can also be used for differential expression/2-class data.") + (license license:gpl3))) + +(define-public r-bayesspace + (package + (name "r-bayesspace") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesSpace" version)) + (sha256 + (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105")))) + (properties `((upstream-name . "BayesSpace"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocfilecache + r-biocsingular + r-coda + r-dirichletreg + r-ggplot2 + r-matrix + r-mclust + r-purrr + r-rcpp + r-rcpparmadillo + r-rcppdist + r-rcppprogress + r-rcurl + r-rhdf5 + r-s4vectors + r-scales + r-scater + r-scran + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://www.ezstatconsulting.com/BayesSpace/") + (synopsis "Clustering and resolution enhancement of spatial transcriptomes") + (description + "This package provides tools for clustering and enhancing the resolution +of spatial gene expression experiments. BayesSpace clusters a low-dimensional +representation of the gene expression matrix, incorporating a spatial prior to +encourage neighboring spots to cluster together. The method can enhance the +resolution of the low-dimensional representation into \"sub-spots\", for which +features such as gene expression or cell type composition can be imputed.") + (license license:expat))) + +(define-public r-baynorm + (package + (name "r-baynorm") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bayNorm" version)) + (sha256 + (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq")))) + (properties `((upstream-name . "bayNorm"))) + (build-system r-build-system) + (propagated-inputs + (list r-bb + r-biocparallel + r-dosnow + r-fitdistrplus + r-foreach + r-iterators + r-locfit + r-mass + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/WT215/bayNorm") + (synopsis "Single-cell RNA sequencing data normalization") + (description + "The bayNorm package is used for normalizing single-cell RNA-seq data. +The main function is @code{bayNorm}, which is a wrapper function for gene +specific prior parameter estimation and normalization. The input is a matrix +of scRNA-seq data with rows different genes and coloums different cells. The +output is either point estimates from posterior (2D array) or samples from +posterior (3D array).") + (license license:gpl2+))) + +(define-public r-bbcanalyzer + (package + (name "r-bbcanalyzer") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BBCAnalyzer" version)) + (sha256 + (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1")))) + (properties `((upstream-name . "BBCAnalyzer"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomicranges + r-iranges + r-rsamtools + r-summarizedexperiment + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BBCAnalyzer") + (synopsis "Visualizing base counts") + (description + "BBCAnalyzer is a package for visualizing the relative or absolute number +of bases, deletions and insertions at defined positions in sequence alignment +data available as bam files in comparison to the reference bases. Markers for +the relative base frequencies, the mean quality of the detected bases, known +mutations or polymorphisms and variants called in the data may additionally be +included in the plots.") + (license license:lgpl3))) + +(define-public r-bcrank + (package + (name "r-bcrank") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BCRANK" version)) + (sha256 + (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9")))) + (properties `((upstream-name . "BCRANK"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings)) + (home-page "https://bioconductor.org/packages/BCRANK") + (synopsis "Predicting binding site consensus from ranked DNA sequences") + (description + "This package provides functions and classes for de novo prediction of +transcription factor binding consensus by heuristic search.") + (license license:gpl2))) + (define-public r-biocthis (package (name "r-biocthis") - (version "1.10.3") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1v0qrypdzl1bg85k8i7qamb6709cgk4ypmisjh6bn5r36nqd5qx4")))) + "0lxcsw70ib8wvkp3ii1l8vd4g2ddhj6g0x22dwcmwacr2myk3bg8")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -22331,14 +23722,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "18j70ma85qb42qqpzz8fw3g4x6cav4j0pc2ab5ym22791dr8izck")))) + "18w062s0wwdisl6a9a79in6h4052x3janinc5isip0x6p9g9d9bk")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -22377,14 +23768,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "04kl2432wq6ybdhispvp98ylgyk3kkhmjx1nxdvcal7bfpy2vskk")))) + "1ccnrz8rkg533kil3sc8wnjqsmiyrpqqmk7av7ls01avglcjdjq1")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -22406,14 +23797,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6")))) + "16finp6q89n6x5q2v1khpfp5ys7d4dvlh3kacv5qbdh1bsb3fpax")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -22426,14 +23817,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r")))) + "04ckv1y5iqawd0dvnn0bbpnmyys0ivcmf0my6dld3hib3idjzwfx")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -22448,14 +23839,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.38.0") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) + "1imni8lpjzf53w2q34ql0j9rwq6drbzxvs0nhzf6s172iqym2hq3")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (arguments @@ -22482,14 +23873,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.8.7") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0yvd05yikvblnhimnmn4srcsimab4qml5k582n0c9h4rppffmvy4")))) + "0pq5fiacb2x8l5jk3p6bnha9bcwg91grpklgx2nirrlwwr80gf2h")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -22538,14 +23929,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1")))) + "122rj6rg4j9q9brhxyrbkc91fml3davk044s2yxwyjnwn2yjw0bq")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -22567,14 +23958,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4")) + "1rbb36v64b9xbk2dsf6wsyrhwwbkysrj8fp1g22y3gisdk170sg8")) (snippet '(delete-file "inst/datatables/js/jquery.dataTables.min.js")))) (properties `((upstream-name . "BioNetStat"))) @@ -22622,14 +24013,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw")))) + "15kmg102259h2yl3b6ncq2p545kdac4hk4kwm1s5492y5rg7qkla")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -22648,14 +24039,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "0lqnxaycrva2092h4swmk6na2pq2kp951dmicyw399djd1i7yj50")))) + "1bbjfv3bi20xlk8h7r5ipav6mfs27lmj0zjb5mk1gmp071dmnk0y")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -22678,14 +24069,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1hjkhwbld8m52lsy2ba6cnp02n0xykaxm9650r5zmzry38dw9nb5")))) + "0h796sxv7fvwx9m8ikamf3bvaac7rimp33lv1j3ngsjifigdkvfy")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -22720,14 +24111,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3")))) + "0afpzr52mf2ab7gr9swdf6609787ymw8s8wksis0d4ap0y0wdgg0")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -22766,13 +24157,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "1vxy2106rzygy0dr38wmw84zrqp9gsvaphliikdmhx0n2gv6xhd1")))) + "0rvnwbknvwksm50f4rw9965gnhy13rjgdfvv428xsqixgkkkyrf6")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs @@ -22803,14 +24194,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1lxrirgy42xnpdj7b2nrabbki33an8ri6j1mgxp3jn4h0a88c280")))) + "0z53vh5qirkyn7yw3g2m2kj6dzii96l81vc8j59n2dl7p602l9a2")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -22849,13 +24240,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "086nh0m82gjlxyg6i230wpkin4zc3a7cfla0qzvj28h0n8irkm5r")))) + "0i4ln95ayl1irr8sr3639x35ilysdi663kksw7g93q1ry91yav8r")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -22868,13 +24259,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.8.2") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "13ac98jj03vkzrc1ghrs98qrfvr74wz099w26lgc7jw2yxj575as")))) + (base32 "1wbzb4kh7bzsvixr3vxzih9rfkpjx00f33i0yl0dqj0yixnrghwr")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -22893,6 +24284,7 @@ interest on transformed methylation proportions.") r-jsonlite r-later r-logger + r-lubridate r-magrittr r-progress r-purrr @@ -22902,6 +24294,7 @@ interest on transformed methylation proportions.") r-rlang r-rmarkdown r-rvest + r-stringi r-stringr r-tibble r-tidyr @@ -22923,14 +24316,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "07nak6mfw9m8ldl336sqgkl3638ibv1hxwd89hwxdrn914wz3hw3")))) + "1q90p14qj5plz6cbvwxq875y29in6jg7adyni5wd33pf9i4gsxzi")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -22975,13 +24368,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.28.3") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "1hh09ya4jg062k1ibp1cpvdrgv6gwr95ch57iycgd3cjc5g0xhii")))) + (base32 "1k8xiv4bmil420176ckfda2r6y0s46dk1cm8dbywav86q28bmzzx")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -23030,13 +24423,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6")))) + "1dawkp681pz9hf7fp2nag9pcfxx5rq0z4j9czlalf0sylsjbirkd")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -23069,14 +24462,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.18.3") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "01s8x8a3rb0a5i599pxc5miz84ssvh10b4vha79nmbhkqccffvml")))) + "1i6d1kw8wqcdzdhzlix29jl5ka8p54nb4b5zyn9ca356nkxf755q")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -23110,13 +24503,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0rmv8f1m8ck97v991wdly3fma2rjczhi974lh7ikwx6rcx6fp9ah")))) + (base32 "06gnpjcniqm8i52xh9xl3nn0wm9nn9rkqd3w3fjv7ii142xypjln")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs |