diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 3943 |
1 files changed, 3087 insertions, 856 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10b70bab069..711b988e7f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,17 +1,18 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2023 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> ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com> +;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,6 +49,7 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) + #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) @@ -505,6 +507,31 @@ ID and species. It is used by functions in the GenomeInfoDb package.") information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) +(define-public r-hdo-db + (package + (name "r-hdo-db") + (version "0.99.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDO.db" version 'annotation)) + (sha256 + (base32 + "14ngyxailmxrbxqqi9m7mchqcvchmbg7zm34i8a927b20s6z4z61")))) + (properties `((upstream-name . "HDO.db"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi)) + (native-inputs + (list r-knitr)) + (home-page "https://bioconductor.org/packages/HDO.db") + (synopsis "Annotation maps describing the entire Human Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Human Disease Ontology. The annotation data comes from +@url{Humam Disease Ontology repository, +https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") @@ -1265,6 +1292,26 @@ from Illumina 450k methylation arrays.") biscuiteer.") (license license:gpl3))) +(define-public r-breakpointrdata + (package + (name "r-breakpointrdata") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointRdata" version 'experiment)) + (sha256 + (base32 + "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn")))) + (properties `((upstream-name . "breakpointRdata"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/breakpointRdata") + (synopsis "Strand-seq data for demonstration purposes") + (description + "This package is a collection of Strand-seq data. The main purpose is to +demonstrate functionalities of the @code{breakpointR} package.") + (license license:expat))) + (define-public r-celldex (package (name "r-celldex") @@ -1384,6 +1431,29 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-macrophage + (package + (name "r-macrophage") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "macrophage" version + 'experiment)) + (sha256 + (base32 + "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms")))) + (properties `((upstream-name . "macrophage"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/macrophage") + (synopsis "Human macrophage immune response data") + (description + "This package provides the output of running @code{Salmon} on a set of 24 +RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and +gene expression indicate a role for enhancer priming in immune response\", published +in Nature Genetics, January 2018.") + (license license:gpl2+))) + (define-public r-msdata (package (name "r-msdata") @@ -1605,19 +1675,43 @@ cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and contro TCGAbiolinksGUI package.") (license license:gpl3))) +(define-public r-tximportdata + (package + (name "r-tximportdata") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximportData" version + 'experiment)) + (sha256 + (base32 + "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy")))) + (properties `((upstream-name . "tximportData"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/tximportData") + (synopsis "Data for the tximport package") + (description + "This package provides the output of running various transcript abundance +quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The +quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon} +and @code{Sailfish}. Alevin example output is also included.") + (license license:gpl2+))) + + ;;; Packages (define-public r-abarray (package (name "r-abarray") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r")))) + "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -1637,13 +1731,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv")))) + "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -1666,13 +1760,13 @@ ranking by fold-change and visualization.") (define-public r-adam (package (name "r-adam") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) + "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -1701,13 +1795,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) + "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -1749,13 +1843,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) + "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -1798,13 +1892,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) + "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -1826,13 +1920,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq")))) + "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -1854,13 +1948,13 @@ expression values are known.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf")))) + "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -1879,13 +1973,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9")))) + "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -1906,13 +2000,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) + "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -1940,13 +2034,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) + "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -1962,13 +2056,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys")))) + "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs @@ -2007,13 +2101,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) + "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -2034,16 +2128,87 @@ using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aims + (package + (name "r-aims") + (version "1.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AIMS" version)) + (sha256 + (base32 + "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1")))) + (properties `((upstream-name . "AIMS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071)) + (home-page "https://git.bioconductor.org/packages/AIMS") + (synopsis + "Absolute assignment of breast cancer intrinsic molecular subtype") + (description + "This package contains an implementation of @code{AIMS} -- Absolute +Intrinsic Molecular Subtyping. It contains necessary functions to assign the +five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, +Basal-like, Normal-like). Assignments could be done on individual samples as +well as on dataset of gene expression data.") + (license license:artistic2.0))) + +(define-public r-airpart + (package + (name "r-airpart") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "airpart" version)) + (sha256 + (base32 + "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl")))) + (properties `((upstream-name . "airpart"))) + (build-system r-build-system) + (propagated-inputs + (list r-apeglm + r-clue + r-complexheatmap + r-dplyr + r-dynamictreecut + r-emdbook + r-forestplot + r-ggplot2 + r-lpsolve + r-matrixstats + r-mclust + r-pbapply + r-plyr + r-rcolorbrewer + r-rlang + r-s4vectors + r-scater + r-singlecellexperiment + r-smurf + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/airpart") + (synopsis "Differential cell-type-specific allelic imbalance") + (description + "The airpart package identifies sets of genes displaying differential +cell-type-specific allelic imbalance across cell types or states, utilizing +single-cell allelic counts. It makes use of a generalized fused lasso with +binomial observations of allelic counts to partition cell types by their +allelic imbalance. Alternatively, a nonparametric method for partitioning +cell types is offered. The package includes a number of visualizations and +quality control functions for examining single cell allelic imbalance +datasets.") + (license license:gpl2))) + (define-public r-amountain (package (name "r-amountain") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) + "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -2058,16 +2223,63 @@ conditions or various species. @code{AMOUNTAIN} aims to search active modules in multi-layer WGCN using a continuous optimization approach.") (license license:gpl2+))) +(define-public r-amplican + (package + (name "r-amplican") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "amplican" version)) + (sha256 + (base32 + "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij")))) + (properties `((upstream-name . "amplican"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-biostrings + r-clustercrit + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggthemes + r-gridextra + r-gtable + r-iranges + r-knitr + r-matrix + r-matrixstats + r-rcpp + r-rmarkdown + r-s4vectors + r-shortread + r-stringr + r-waffle)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/valenlab/amplican") + (synopsis "Automated analysis of CRISPR experiments") + (description + "The package performs alignment of the amplicon reads, normalizes +gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) +and presents the results in the form of aggregated reports. Data and +statistics can be broken down by experiments, barcodes, user defined groups, +guides and amplicons allowing for quick identification of potential +problems.") + (license license:gpl3))) + (define-public r-amaretto (package (name "r-amaretto") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -2113,13 +2325,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) + "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -2140,16 +2352,408 @@ of Medical Research. The goal is to provide a standard library for quantitative analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) +(define-public r-ancombc + (package + (name "r-ancombc") + (version "2.0.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANCOMBC" version)) + (sha256 + (base32 + "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) + (properties `((upstream-name . "ANCOMBC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cvxr + r-desctools + r-doparallel + r-dorng + r-dplyr + r-emmeans + r-energy + r-foreach + r-hmisc + r-lme4 + r-lmertest + r-magrittr + r-mass + r-mia + r-nloptr + r-rdpack + r-rlang + r-rngtools + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/FrederickHuangLin/ANCOMBC") + (synopsis "Analysis of compositions of microbiomes with bias correction") + (description + "@code{ANCOMBC} is a package containing @dfn{differential abundance} (DA) +and correlation analyses for microbiome data. Specifically, the package +includes @dfn{Analysis of Compositions of Microbiomes with Bias +Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM) +for DA analysis, and @dfn{Sparse Estimation of Correlations among +Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically +subject to two sources of biases: unequal sampling fractions (sample-specific +biases) and differential sequencing efficiencies (taxon-specific biases). +Methodologies included in the @code{ANCOMBC} package were designed to correct +these biases and construct statistically consistent estimators.") + (license license:artistic2.0))) + +(define-public r-animalcules + (package + (name "r-animalcules") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "animalcules" version)) + (sha256 + (base32 + "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr")))) + (properties `((upstream-name . "animalcules"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-assertthat + r-biomformat + r-caret + r-covr + r-deseq2 + r-dplyr + r-dt + r-forcats + r-ggplot2 + r-glmnet + r-gunifrac + r-lattice + r-limma + r-magrittr + r-matrix + r-multiassayexperiment + r-plotly + r-plotroc + r-rentrez + r-reshape2 + r-s4vectors + r-scales + r-shiny + r-shinyjs + r-summarizedexperiment + r-tibble + r-tsne + r-umap + r-vegan + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/compbiomed/animalcules") + (synopsis "Interactive microbiome analysis toolkit") + (description + "Animalcules is an R package for utilizing up-to-date data analytics, +visualization methods, and machine learning models to provide users an +easy-to-use interactive microbiome analysis framework. It can be used as a +standalone software package or users can explore their data with the +accompanying interactive R Shiny application. Traditional microbiome analysis +such as alpha/beta diversity and differential abundance analysis are enhanced, +while new methods like biomarker identification are introduced by animalcules. +Powerful interactive and dynamic figures generated by animalcules enable users +to understand their data better and discover new insights.") + (license license:artistic2.0))) + +(define-public r-anvil + (package + (name "r-anvil") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnVIL" version)) + (sha256 + (base32 + "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv")))) + (properties `((upstream-name . "AnVIL"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocmanager + r-dplyr + r-dt + r-futile-logger + r-htmltools + r-httr + r-jsonlite + r-miniui + r-rapiclient + r-rlang + r-shiny + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnVIL") + (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") + (description + "The AnVIL is a cloud computing resource developed in part by the +National Human Genome Research Institute. The AnVIL package provides end-user +and developer functionality. AnVIL provides fast binary package installation, +utilities for working with Terra/AnVIL table and data resources, and +convenient functions for file movement to and from Google cloud storage. For +developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, +Dockstore, and Gen3 RESTful programming interface, including helper functions +to transform JSON responses to formats more amenable to manipulation in R.") + (license license:artistic2.0))) + +(define-public r-aldex2 + (package + (name "r-aldex2") + (version "1.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ALDEx2" version)) + (sha256 + (base32 + "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf")))) + (properties `((upstream-name . "ALDEx2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ggloor/ALDEx_bioc") + (synopsis "Analysis of differential abundance taking sample variation into account") + (description + "This package provides a differential abundance analysis for the +comparison of two or more conditions. Useful for analyzing data from standard +RNA-seq or meta-RNA-seq assays as well as selected and unselected values from +in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer +abundance from counts, optimized for three or more experimental replicates. +The method infers biological and sampling variation to calculate the expected +false discovery rate, given the variation, based on a Wilcoxon Rank Sum test +and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a +correlation test. All tests report p-values and Benjamini-Hochberg corrected +p-values. ALDEx2 also calculates expected standardized effect sizes for +paired or unpaired study designs.") + ;; The code for the function "rdirichlet" is from the R package + ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the + ;; package's LICENSE is specified as GPL-3. + (license (list license:agpl3+ license:gpl2+ license:gpl3)))) + +(define-public r-alevinqc + (package + (name "r-alevinqc") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alevinQC" version)) + (sha256 + (base32 + "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2")))) + (properties `((upstream-name . "alevinQC"))) + (build-system r-build-system) + (propagated-inputs + (list r-cowplot + r-dplyr + r-dt + r-ggally + r-ggplot2 + r-rcpp + r-rjson + r-rlang + r-rmarkdown + r-shiny + r-shinydashboard + r-tximport)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/csoneson/alevinQC") + (synopsis "Quality control reports for @code{Alevin} output") + (description + "The package @code{r-alevinqc} generates quality control reports +summarizing the output from an @code{alevin} run. The reports can be +generated as HTML or PDF files, or as Shiny applications.") + (license license:expat))) + +(define-public r-alphabeta + (package + (name "r-alphabeta") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlphaBeta" version)) + (sha256 + (base32 + "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b")))) + (properties `((upstream-name . "AlphaBeta"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-dplyr + r-expm + r-ggplot2 + r-gtools + r-igraph + r-optimx + r-plotly + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AlphaBeta") + (synopsis "Estimate epimutation rates and spectra from DNA methylations in plants") + (description + "The package @code{AlphaBeta} is a computational method for estimating +epimutation rates and spectra from high-throughput DNA methylation data in +plants. The method has been specifically designed to: + +@itemize +@item analyze @emph{germline} epimutations in the context of + multi-generational mutation accumulation lines; +@item analyze @emph{somatic} epimutations in the context of plant development + and aging. +@end itemize") + (license license:gpl3))) + +(define-public r-alpine + (package + (name "r-alpine") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "alpine" version)) + (sha256 + (base32 + "0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0")))) + (properties `((upstream-name . "alpine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-speedglm + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/alpine") + (synopsis "Modeling and correcting fragment sequence bias") + (description + "The package @code{alpine} helps to model bias parameters and then using +those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a +package for estimating and visualizing many forms of sample-specific biases that +can arise in RNA-seq, including fragment length distribution, positional bias on +the transcript, read start bias (random hexamer priming), and fragment GC-content +(amplification). It also offers bias-corrected estimates of transcript +abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million +mapped reads). It is currently designed for un-stranded paired-end RNA-seq +data.") + (license license:gpl2+))) + +(define-public r-alpsnmr + (package + (name "r-alpsnmr") + (version "4.0.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlpsNMR" version)) + (sha256 + (base32 + "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + (properties `((upstream-name . "AlpsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-baseline + r-biocparallel + r-dplyr + r-fs + r-future + r-generics + r-ggplot2 + r-glue + r-htmltools + r-magrittr + r-matrixstats + r-mixomics + r-pcapp + r-purrr + r-readxl + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-signal + r-speaq + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://sipss.github.io/AlpsNMR/") + (synopsis "Automated spectral processing system for NMR") + (description + "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data +directories both zipped and unzipped. It provides automated and efficient +signal processing for untargeted NMR metabolomics. It is able to interpolate +the samples, detect outliers, exclude regions, normalize, detect peaks, align +the spectra, integrate peaks, manage metadata and visualize the spectra. +After spectra processing, it can apply multivariate analysis on extracted +data. Efficient plotting with 1-D data is also available. Basic reading of +1D ACD/Labs exported JDX samples is also available.") + (license license:expat))) + +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with Affymetrix GeneChip short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read R connections in the FASTA format and it can +create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl")))) + "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2185,13 +2789,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj")))) + "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs @@ -2213,13 +2817,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs @@ -2247,13 +2851,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -2270,17 +2874,698 @@ reproducible gene expression signatures capable of accurately distinguishing tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayexpress + (package + (name "r-arrayexpress") + (version "1.57.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ArrayExpress" version)) + (sha256 + (base32 + "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6")))) + (properties `((upstream-name . "ArrayExpress"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-limma + r-oligo + r-xml)) + (home-page "https://bioconductor.org/packages/ArrayExpress") + (synopsis "Building R objects from ArrayExpress datasets") + (description + "This package offers the possibility to access the ArrayExpress repository +at @dfn{EBI} (European Bioinformatics Institute) and build Bioconductor data +structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") + (license license:artistic2.0))) + +(define-public r-asafe + (package + (name "r-asafe") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be +used to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate +ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an +@dfn{SNP} (single nucleotide polymorphism) from genotypes and ancestry +pairs.") + (license license:artistic2.0))) + +(define-public r-aseb + (package + (name "r-aseb") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASEB" version)) + (sha256 + (base32 + "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa")))) + (properties `((upstream-name . "ASEB"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/ASEB") + (synopsis "Predict acetylated lysine sites") + (description + "ASEB is an R package to predict lysine sites that can be acetylated by a +specific @dfn{KAT} (K-acetyl-transferases) family. Lysine acetylation is a +well-studied posttranslational modification on kinds of proteins. About four +thousand lysine acetylation sites and over 20 lysine KATs have been +identified. However, which KAT is responsible for a given protein or lysine +site acetylation is mostly unknown. In this package, we use a +@dfn{GSEA}-like (Gene Set Enrichment Analysis) method to make predictions. +GSEA method was developed and successfully used to detect coordinated +expression changes and find the putative functions of the long non-coding +RNAs.") + (license license:gpl3+))) + +(define-public r-asgsca + (package + (name "r-asgsca") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASGSCA" version)) + (sha256 + (base32 + "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i")))) + (properties `((upstream-name . "ASGSCA"))) + (build-system r-build-system) + (propagated-inputs (list r-mass r-matrix)) + (home-page "https://bioconductor.org/packages/ASGSCA") + (synopsis "Analysis of associations between multiple genotypes and traits") + (description + "The package @dfn{ASGSCA} (Association Study using Generalized Structured +Component Analysis) provides tools to model and test the association between +multiple genotypes and multiple traits, taking into account the prior +biological knowledge. Genes, and clinical pathways are incorporated in the +model as latent variables.") + (license license:gpl3))) + +(define-public r-asics + (package + (name "r-asics") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASICS" version)) + (sha256 + (base32 + "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7")))) + (properties `((upstream-name . "ASICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-ggplot2 + r-glmnet + r-gridextra + r-matrix + r-mvtnorm + r-pepsnmr + r-plyr + r-quadprog + r-ropls + r-summarizedexperiment + r-zoo)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASICS") + (synopsis "Automatic statistical identification in complex spectra") + (description + "ASICS quantifies concentration of metabolites in a complex spectrum. +The identification of metabolites is performed by fitting a mixture model to +the spectra of the library with a sparse penalty.") + (license license:gpl2+))) + +(define-public r-aspli + (package + (name "r-aspli") + (version "2.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASpli" version)) + (sha256 + (base32 + "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k")))) + (properties `((upstream-name . "ASpli"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-biocstyle + r-data-table + r-dt + r-edger + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gviz + r-htmltools + r-igraph + r-iranges + r-limma + r-mass + r-pbmcapply + r-rsamtools + r-s4vectors + r-tidyr + r-upsetr)) + (home-page "https://bioconductor.org/packages/ASpli") + (synopsis "Analysis of alternative splicing using RNA-Seq") + (description + "@dfn{AS} (alternative splicing) is a common mechanism of +post-transcriptional gene regulation in eukaryotic organisms that expands the +functional and regulatory diversity of a single gene by generating multiple +mRNA isoforms that encode structurally and functionally distinct proteins. +ASpli is an integrative pipeline and user-friendly R package that facilitates +the analysis of changes in both annotated and novel AS events. ASpli +integrates several independent signals in order to deal with the complexity +that might arise in splicing patterns.") + ;; The authors didn't specify any GPL version in description or in the + ;; sources. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-assessorf + (package + (name "r-assessorf") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AssessORF" version)) + (sha256 + (base32 + "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml")))) + (properties `((upstream-name . "AssessORF"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-decipher + r-genomicranges + r-iranges)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AssessORF") + (synopsis "Assess gene predictions using proteomics and evolutionary conservation") + (description + "In order to assess the quality of a set of predicted genes for a genome, +evidence must first be mapped to that genome. Next, each gene must be +categorized based on how strong the evidence is for or against that gene. The +AssessORF package provides the functions and class structures necessary for +accomplishing those tasks, using proteomics hits and evolutionarily conserved +start codons as the forms of evidence.") + (license license:gpl3))) + +(define-public r-asset + (package + (name "r-asset") + (version "2.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASSET" version)) + (sha256 + (base32 + "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2")))) + (properties `((upstream-name . "ASSET"))) + (build-system r-build-system) + (propagated-inputs (list r-mass r-msm r-rmeta)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASSET") + (synopsis + "Subset-based association analysis of heterogeneous traits and subtypes") + (description + "This package is an R program for the subset-based analysis of +heterogeneous traits and disease subtypes. ASSET allows the user to search +through all possible subsets of z-scores to identify the subset of traits +giving the best meta-analyzed z-score. Further, it returns a p-value +adjusting for the multiple-testing involved in the search. It also allows for +searching for the best combination of disease subtypes associated with each +variant.") + (license license:gpl2))) + +(define-public r-atena + (package + (name "r-atena") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atena" version)) + (sha256 + (base32 + "1a3qv66caz2pg67ff9c5424pygsgqnfx67ybzc3zkzaw4fj8cp54")))) + (properties `((upstream-name . "atena"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-s4vectors + r-scales + r-sparsematrixstats + r-squarem + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/functionalgenomics/atena") + (synopsis "Analysis of transposable elements") + (description + "The atena package quantifies expression of @dfn{TEs} (transposable +elements) from RNA-seq data through different methods, including ERVmap, +TEtranscripts and Telescope. A common interface is provided to use each of +these methods, which consists of building a parameter object, calling the +quantification function with this object and getting a +@code{SummarizedExperiment} object as an output container of the quantified +expression profiles. The implementation allows quantifing TEs and gene +transcripts in an integrated manner.") + (license license:artistic2.0))) + +(define-public r-atsnp + (package + (name "r-atsnp") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "atSNP" version)) + (sha256 + (base32 + "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb")))) + (properties `((upstream-name . "atSNP"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocfilecache + r-biocparallel + r-bsgenome + r-data-table + r-ggplot2 + r-lifecycle + r-motifstack + r-rappdirs + r-rcpp + r-testthat)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sunyoungshin/atSNP") + (synopsis + "Affinity test for identifying regulatory single nucleotide polymorphisms") + (description + "The atSNP package performs affinity tests of motif matches with the +@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and +SNP-led changes in motif matches.") + (license license:gpl2))) + +(define-public r-attract + (package + (name "r-attract") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "attract" version)) + (sha256 + (base32 + "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm")))) + (properties `((upstream-name . "attract"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biobase + r-cluster + r-gostats + r-keggrest + r-limma + r-org-hs-eg-db + r-reactome-db)) + (home-page "https://bioconductor.org/packages/attract") + (synopsis "Finding drivers of Kauffman's attractor landscape") + (description + "This package contains the functions to find the gene expression modules +that represent the drivers of Kauffman's attractor landscape. The modules are +the core attractor pathways that discriminate between different cell types of +groups of interest. Each pathway has a set of synexpression groups, which show +transcriptionally-coordinated changes in gene expression.") + (license license:lgpl2.0+))) + +(define-public r-awfisher + (package + (name "r-awfisher") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AWFisher" version)) + (sha256 + (base32 + "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9")))) + (properties `((upstream-name . "AWFisher"))) + (build-system r-build-system) + (propagated-inputs + (list r-edger + r-limma)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AWFisher") + (synopsis "Fast computing for adaptively weighted fisher's method") + (description + "This package is an implementation of the Adaptively Weighted Fisher's +method, including fast p-value computing, variability index, and +meta-pattern.") + (license license:gpl3))) + +(define-public r-awst + (package + (name "r-awst") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "awst" version)) + (sha256 + (base32 + "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15")))) + (properties `((upstream-name . "awst"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/drisso/awst") + (synopsis "Asymmetric within-sample transformation") + (description + "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that +regularizes RNA-seq read counts and reduces the effect of noise on the +classification of samples. AWST comprises two main steps: standardization and +smoothing. These steps transform gene expression data to reduce the noise of +the lowly expressed features, which suffer from background effects and low +signal-to-noise ratio, and the influence of the highly expressed features, +which may be the result of amplification bias and other experimental +artifacts.") + (license license:expat))) + +(define-public r-baalchip + (package + (name "r-baalchip") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaalChIP" version)) + (sha256 + (base32 + "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n")))) + (properties `((upstream-name . "BaalChIP"))) + (build-system r-build-system) + (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl + (propagated-inputs + (list r-coda + r-doby + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-reshape2 + r-rsamtools + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BaalChIP") + (synopsis + "Analysis of allele-specific transcription factor binding in cancer genomes") + (description + "This package offers functions to process multiple @code{ChIP-seq BAM} +files and detect allele-specific events. It computes allele counts at +individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality +control) steps to remove problematic variants, and utilizes a Bayesian +framework to identify statistically significant allele-specific events. +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-basespacer + (package + (name "r-basespacer") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BaseSpaceR" version)) + (sha256 + (base32 + "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7")))) + (properties `((upstream-name . "BaseSpaceR"))) + (build-system r-build-system) + (propagated-inputs (list r-rcurl r-rjsonio)) + (home-page "https://bioconductor.org/packages/BaseSpaceR") + (synopsis "R SDK for BaseSpace RESTful API") + (description + "This package provides an R interface to Illumina's BaseSpace cloud +computing environment, enabling the fast development of data analysis and +visualization tools. Besides providing an easy to use set of tools for +manipulating the data from BaseSpace, it also facilitates the access to R's +rich environment of statistical and data analysis tools.") + (license license:asl2.0))) + +(define-public r-bac + (package + (name "r-bac") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BAC" version)) + (sha256 + (base32 + "00dkhns9n1x4wmlxjcw75h7iwwk37zlv1c2fi0g1mmsw1xvdjzp6")))) + (properties `((upstream-name . "BAC"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BAC") + (synopsis "Bayesian analysis of Chip-chip experiment") + (description + "This package uses a Bayesian hierarchical model to detect enriched +regions from ChIP-chip experiments. The common goal in analyzing this +ChIP-chip data is to detect DNA-protein interactions from ChIP-chip +experiments. The BAC package has mainly been tested with Affymetrix tiling +array data. However, we expect it to work with other platforms (e.g. Agilent, +Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so +you will have to normalize your data beforehand.") + (license license:artistic2.0))) + +(define-public r-bader + (package + (name "r-bader") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BADER" version)) + (sha256 + (base32 + "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr")))) + (properties `((upstream-name . "BADER"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/BADER") + (synopsis + "Bayesian analysis of differential expression in RNA sequencing data") + (description + "The BADER package is intended for the analysis of RNA sequencing data. +The algorithm fits a Bayesian hierarchical model for RNA sequencing count +data. BADER returns the posterior probability of differential expression for +each gene between two groups A and B. The joint posterior distribution of the +variables in the model can be returned in the form of posterior samples, which +can be used for further down-stream analyses such as gene set enrichment.") + (license license:gpl2))) + +(define-public r-badregionfinder + (package + (name "r-badregionfinder") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BadRegionFinder" version)) + (sha256 + (base32 + "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm")))) + (properties `((upstream-name . "BadRegionFinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomart + r-genomicranges + r-rsamtools + r-s4vectors + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BadRegionFinder") + (synopsis "Identifying regions with bad coverage in sequence alignment data") + (description + "BadRegionFinder is a package for identifying regions with a bad, +acceptable and good coverage in sequence alignment data available as bam +files. The whole genome may be considered as well as a set of target regions. +Various visual and textual types of output are available.") + (license license:lgpl3))) + +(define-public r-bambu + (package + (name "r-bambu") + (version "3.0.5") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bambu" version)) + (sha256 + (base32 + "12rcbspy4ly714cyxbgd5v2m92vasksxm19m6hd4avasrhcr4d6l")))) + (properties `((upstream-name . "bambu"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-bsgenome + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tidyr + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/GoekeLab/bambu") + (synopsis + "Isoform reconstruction and quantification for long read RNA-Seq data") + (description + "This R package is for multi-sample transcript discovery and +quantification using long read RNA-Seq data. You can use bambu after read +alignment to obtain expression estimates for known and novel transcripts and +genes. The output from bambu can directly be used for visualisation and +downstream analysis, such as differential gene expression or transcript +usage.") + (license license:gpl3))) + +(define-public r-bandits + (package + (name "r-bandits") + (version "1.14.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BANDITS" version)) + (sha256 + (base32 + "0dbiz7zgdl3bqrwf4ffb73sc2dd8ygh76fakx5887a14azj8pk8x")))) + (properties `((upstream-name . "BANDITS"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-data-table + r-doparallel + r-dorng + r-drimseq + r-foreach + r-ggplot2 + r-mass + r-r-utils + r-rcpp + r-rcpparmadillo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SimoneTiberi/BANDITS") + (synopsis "Bayesian analysis of differential splicing") + (description + "BANDITS is a Bayesian hierarchical model for detecting differential +splicing of genes and transcripts, via @dfn{DTU} (differential transcript +usage), between two or more conditions. The method uses a Bayesian +hierarchical framework, which allows for sample specific proportions in a +Dirichlet-Multinomial model, and samples the allocation of fragments to the +transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte +Carlo) techniques and a DTU test is performed via a multivariate Wald test on +the posterior densities for the average relative abundance of transcripts.") + (license license:gpl3+))) + +(define-public r-banocc + (package + (name "r-banocc") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "banocc" version)) + (sha256 + (base32 + "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78")))) + (properties `((upstream-name . "banocc"))) + (build-system r-build-system) + (propagated-inputs + (list r-coda + r-mvtnorm + r-rstan + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/banocc") + (synopsis "Bayesian analysis of compositional covariance") + (description + "BAnOCC is a package designed for compositional data, where each sample +sums to one. It infers the approximate covariance of the unconstrained data +using a Bayesian model coded with @code{rstan}. It provides as output the +@code{stanfit} object as well as posterior median and credible interval +estimates for each correlation element.") + (license license:expat))) + +(define-public r-barcodetrackr + (package + (name "r-barcodetrackr") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "barcodetrackR" version)) + (sha256 + (base32 + "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1")))) + (properties `((upstream-name . "barcodetrackR"))) + (build-system r-build-system) + (propagated-inputs + (list r-circlize + r-cowplot + r-dplyr + r-ggdendro + r-ggplot2 + r-ggridges + r-magrittr + r-plyr + r-proxy + r-rcolorbrewer + r-rlang + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/dunbarlabNIH/barcodetrackR") + (synopsis "Functions for analyzing cellular barcoding data") + (description + "This package is developed for the analysis and visualization of clonal +tracking data. The required data is formed by samples and tag abundances in +matrix form, usually from cellular barcoding experiments, integration site +retrieval analyses, or similar technologies.") + (license license:cc0))) + (define-public r-biocversion (package (name "r-biocversion") - (version "3.15.2") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn")))) + "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -2293,13 +3578,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.42.0") + (version "0.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc")))) + "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -2310,16 +3595,88 @@ of Bioconductor.") packages.") (license license:artistic2.0))) +(define-public r-breakpointr + (package + (name "r-breakpointr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointR" version)) + (sha256 + (base32 + "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx")))) + (properties `((upstream-name . "breakpointR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-breakpointrdata + r-cowplot + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/BreakPointR") + (synopsis "Find breakpoints in Strand-seq data") + (description + "This package implements functions for finding breakpoints, plotting and +export of Strand-seq data.") + (license license:expat))) + +(define-public r-cardelino + (package + (name "r-cardelino") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "cardelino" version)) + (sha256 + (base32 + "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs")))) + (properties `((upstream-name . "cardelino"))) + (build-system r-build-system) + (propagated-inputs (list r-combinat + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-ggtree + r-matrix + r-matrixstats + r-pheatmap + r-s4vectors + r-snpstats + r-variantannotation + r-vcfr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/single-cell-genetics/cardelino") + (synopsis "Clone identification from single cell data") + (description + "This package provides methods to infer clonal tree configuration for a +population of cells using single-cell RNA-seq data (scRNA-seq), and possibly +other data modalities. Methods are also provided to assign cells to inferred +clones and explore differences in gene expression between clones. These +methods can flexibly integrate information from imperfect clonal trees +inferred based on bulk exome-seq data, and sparse variant alleles expressed in +scRNA-seq data. A flexible beta-binomial error model that accounts for +stochastic dropout events as well as systematic allelic imbalance is used.") + (license license:gpl3))) + (define-public r-coverageview (package (name "r-coverageview") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp")))) + "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors @@ -2340,13 +3697,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q")))) + "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -2367,17 +3724,80 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-dama + (package + (name "r-dama") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "daMA" version)) + (sha256 + (base32 + "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf")))) + (properties `((upstream-name . "daMA"))) + (build-system r-build-system) + (propagated-inputs (list r-mass)) + (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html") + (synopsis + "Efficient design and analysis of factorial two-colour microarray data") + (description + "This package contains functions for the efficient design of factorial +two-colour microarray experiments and for the statistical analysis of +factorial microarray data.") + (license license:gpl2+))) + +(define-public r-damefinder + (package + (name "r-damefinder") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DAMEfinder" version)) + (sha256 + (base32 + "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) + (properties `((upstream-name . "DAMEfinder"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bumphunter + r-cowplot + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-plyr + r-readr + r-reshape2 + r-rsamtools + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DAMEfinder") + (synopsis "Differential allelicly methylated regions") + (description + "This package offers functionality for taking methtuple or Bismark +outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and +compute @acronym{DAMEs, Differential Allelicly MEthylated} regions. It also +offers nice visualization of methyl-circle plots.") + (license license:expat))) + (define-public r-dearseq (package (name "r-dearseq") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1")))) + "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -2390,6 +3810,7 @@ used visualizations.") r-pbapply r-reshape2 r-rlang + r-scattermore r-statmod r-survey r-tibble @@ -2405,16 +3826,55 @@ heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data.") (license license:gpl2))) +(define-public r-debcam + (package + (name "r-debcam") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "debCAM" version)) + (sha256 + (base32 + "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) + (properties `((upstream-name . "debCAM"))) + (build-system r-build-system) + (inputs (list openjdk)) + (propagated-inputs + (list r-apcluster + r-biobase + r-biocparallel + r-corpcor + r-dmwr2 + r-geometry + r-nmf + r-nnls + r-pcapp + r-rjava + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/debCAM") + (synopsis "Deconvolution by convex analysis of mixtures") + (description + "This package is an R implementation for fully unsupervised deconvolution +of complex tissues. DebCAM provides basic functions to perform unsupervised +deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis +of Mixtures} and some auxiliary functions to help understand the +subpopulation- specific results. It also implements functions to perform +supervised deconvolution based on prior knowledge of molecular markers, S +matrix or A matrix. Combining molecular markers from CAM and from prior +knowledge can achieve semi-supervised deconvolution of mixtures.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5")))) + "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -2429,16 +3889,187 @@ set analyses, and can deal with repeated or longitudinal data.") biological sequences.") (license license:gpl3))) +(define-public r-deco + (package + (name "r-deco") + (version "1.13.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "deco" version)) + (sha256 + (base32 + "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw")))) + (properties `((upstream-name . "deco"))) + (build-system r-build-system) + (propagated-inputs + (list r-ade4 + r-annotationdbi + r-biobase + r-biocparallel + r-biocstyle + r-cluster + r-foreign + r-gdata + r-ggplot2 + r-gplots + r-gridextra + r-limma + r-locfit + r-made4 + r-rcolorbrewer + r-reshape2 + r-scatterplot3d + r-sfsmisc + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/fjcamlab/deco") + (synopsis "Decomposing heterogeneous cohorts using omic data profiling") + (description + "This package discovers differential features in hetero- and homogeneous +omic data by a two-step method including subsampling LIMMA and NSCA. DECO +reveals feature associations to hidden subclasses not exclusively related to +higher deregulation levels.") + (license license:gpl3+))) + +(define-public r-decomplexdisease + (package + (name "r-decomplexdisease") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DEComplexDisease" version)) + (sha256 + (base32 + "12gw9b0gdwyih51j2gzay6vxhycgc52n8svd0slv6wsbw5rc19lh")))) + (properties `((upstream-name . "DEComplexDisease"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-edger + r-rcpp + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DEComplexDisease") + (synopsis "Investigations of complex diseases by bi-clustering analysis") + (description + "DEComplexDisease is designed to find the @acronym{DEGs, Differential +Expressed Genes} for complex disease, which is characterized by the +heterogeneous genomic expression profiles. Different from the established DEG +analysis tools, it does not assume the patients of complex diseases to share +the common DEGs. By applying a bi-clustering algorithm, DEComplexDisease +finds the DEGs shared by as many patients. Applying the DEComplexDisease +analysis results, users are possible to find the patients affected by the same +mechanism based on the shared signatures.") + (license license:gpl3))) + +(define-public r-decomptumor2sig + (package + (name "r-decomptumor2sig") + (version "2.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decompTumor2Sig" version)) + (sha256 + (base32 + "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd")))) + (properties `((upstream-name . "decompTumor2Sig"))) + (build-system r-build-system) + (inputs (list perl)) ;script/extractSpecColumns.pl + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-data-table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-matrix + r-plyr + r-quadprog + r-readxl + r-s4vectors + r-summarizedexperiment + r-txdb-hsapiens-ucsc-hg19-knowngene + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://rmpiro.net/decompTumor2Sig/") + (synopsis "Decomposition of individual tumors into mutational signatures") + (description + "The package uses quadratic programming for signature refitting, i.e., to +decompose the mutation catalog from an individual tumor sample into a set of +given mutational signatures (either Alexandrov-model signatures or +Shiraishi-model signatures), computing weights that reflect the contributions +of the signatures to the mutation load of the tumor.") + (license license:gpl2))) + +(define-public r-deconrnaseq + (package + (name "r-deconrnaseq") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DeconRNASeq" version)) + (sha256 + (base32 + "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4")))) + (properties `((upstream-name . "DeconRNASeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-limsolve + r-pcamethods)) + (home-page "https://bioconductor.org/packages/DeconRNASeq") + (synopsis + "Deconvolution of heterogeneous tissue samples for mRNA-Seq data") + (description + "DeconSeq is an R package for deconvolution of heterogeneous tissues +based on mRNA-Seq data. It models the expression levels from heterogeneous +cell populations in mRNA-Seq as the weighted average of expression from +different constituting cell types and predicted cell type proportions of +single expression profiles.") + (license license:gpl2))) + +(define-public r-decontam + (package + (name "r-decontam") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decontam" version)) + (sha256 + (base32 + "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82")))) + (properties `((upstream-name . "decontam"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/benjjneb/decontam") + (synopsis + "Identification of contaminants in marker-gene and metagenomics data") + (description + "This package offers simple statistical identification of contaminating +sequence features in marker-gene or metagenomics data. It works on any kind +of feature derived from environmental sequencing data (e.g. ASVs, OTUs, +taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced +negative control samples.") + (license license:artistic2.0))) + (define-public r-deconvr (package (name "r-deconvr") - (version "1.2.0") + (version "1.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3")))) + "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -2454,6 +4085,7 @@ biological sequences.") r-mass r-matrixstats r-methylkit + r-minfi r-nnls r-quadprog r-rsq @@ -2476,13 +4108,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m")))) + (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs @@ -2517,13 +4149,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn")))) + "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -2553,13 +4185,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.22.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy")))) + "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -2583,13 +4215,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5")))) + (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -2608,13 +4240,13 @@ calculation in parallel.") (define-public r-drimseq (package (name "r-drimseq") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l")))) + (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -2643,13 +4275,13 @@ results.") (define-public r-bluster (package (name "r-bluster") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8")))) + "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -2673,13 +4305,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3")))) + "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -2697,14 +4329,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + "11hgw6c67gd3ih5q14a520sjmnlv56qw19z0i6s5pz2slmgflpry")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -2728,15 +4360,16 @@ arbitrary genomic intervals along chromosomal ideogram.") r-gplots r-gridextra r-hiddenmarkov - r-leiden + r-igraph r-matrix r-paralleldist r-phyclust r-rann r-rcolorbrewer - r-reshape + r-reshape2 r-rjags r-singlecellexperiment + r-seurat r-summarizedexperiment r-tidyr)) (native-inputs (list r-knitr)) @@ -2756,13 +4389,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3")))) + "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -2784,13 +4417,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd")))) + (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -2942,18 +4575,19 @@ mapping.") (define-public r-nmf (package (name "r-nmf") - (version "0.24.0") + (version "0.25") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628")))) + "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs (list r-cluster + r-codetools r-biobase r-biocmanager r-bigmemory ; suggested @@ -2964,7 +4598,6 @@ mapping.") r-foreach r-ggplot2 r-gridbase - r-pkgmaker r-rcolorbrewer r-registry r-reshape2 @@ -2986,14 +4619,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7")))) + "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -3014,14 +4647,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0")))) + "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -3035,14 +4668,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda")))) + "1bg7iqasvfsgd9x3ykgpblqnz1q06g3ifmzj4jf2kn8kxj63wfbl")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -3080,14 +4713,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p")))) + "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -3103,14 +4736,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww")))) + "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -3145,14 +4778,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp")))) + "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -3169,14 +4802,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils")))) + "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -3197,14 +4830,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g")))) + "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -3224,13 +4857,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn")))) + "1srv0jizmwgmsmgb9cfgy5nbgd3jsgxgzzax6wfsahckb5zihrqp")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -3254,13 +4887,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald")))) + "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -3279,14 +4912,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8")))) + "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -3311,14 +4944,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs")))) + "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -3352,14 +4985,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys")))) + "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -3376,14 +5009,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky")))) + "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -3406,13 +5039,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv")))) + "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -3428,13 +5061,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg")))) + "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -3513,13 +5146,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.30.3") + (version "1.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92")))) + "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -3531,18 +5164,16 @@ only one command.") ;; Remove generated documentation. (for-each delete-file '("inst/doc/BiocParallel_BatchtoolsParam.pdf" - "inst/doc/Introduction_To_BiocParallel.pdf" "inst/doc/Errors_Logs_And_Debugging.pdf" "inst/doc/BiocParallel_BatchtoolsParam.R" "inst/doc/Introduction_To_BiocParallel.R" - "inst/doc/Errors_Logs_And_Debugging.R")) + "inst/doc/Errors_Logs_And_Debugging.R" + "inst/doc/Random_Numbers.R")) ;; Remove time-dependent macro (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" - "inst/doc/Introduction_To_BiocParallel.Rnw" "inst/doc/Errors_Logs_And_Debugging.Rnw" "vignettes/BiocParallel_BatchtoolsParam.Rnw" - "vignettes/Introduction_To_BiocParallel.Rnw" "vignettes/Errors_Logs_And_Debugging.Rnw") (("\\today") "later")) @@ -3552,7 +5183,7 @@ only one command.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-bh r-codetools r-futile-logger r-snow)) + (list r-bh r-cpp11 r-codetools r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") @@ -3566,13 +5197,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8")))) + "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -3594,14 +5225,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd")))) + "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -3636,13 +5267,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.64.0") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc")))) + "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -3667,14 +5298,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd")))) + "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -3698,13 +5329,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7")))) + "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3718,6 +5349,7 @@ analysis.") r-genomicranges r-genomicfeatures r-ggplot2 + r-ggvenndiagram r-gplots r-gtools r-dplyr @@ -3744,14 +5376,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i")))) + "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -3770,14 +5402,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65")))) + "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -3810,14 +5442,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.28.0") + (version "2.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb")))) + "1h4cyrjwdazgk49yzi9lvya8bfz9r4cpq19hyzikvc81ia8zdxs6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -3881,26 +5513,26 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.36.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7")))) + "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-genefilter r-geneplotter r-genomicranges r-ggplot2 r-iranges r-locfit + r-matrixstats r-rcpp r-rcpparmadillo r-s4vectors @@ -3919,14 +5551,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am")))) + "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -3964,13 +5596,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb")))) + (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -4002,14 +5634,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx")))) + "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -4029,13 +5661,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4")))) + "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -4073,14 +5705,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws")))) + "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -4113,13 +5745,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.38.4") + (version "3.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6")))) + "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -4138,14 +5770,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc")))) + "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -4183,14 +5815,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy")))) + "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -4210,14 +5842,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b")))) + "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -4238,14 +5870,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.78.0") + (version "1.80.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) + "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) @@ -4262,13 +5894,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93")))) + "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) @@ -4281,13 +5913,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79")))) + "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -4328,13 +5960,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.32.3") + (version "1.34.6") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "17nwcq2ivj3bdibdywfyjq4n6z0djispbh9ahqa55sp31ksq41xh")))) + "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -4355,13 +5987,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz")))) + "0y9yjyzch0cn2j4yrwfp0z8qw3yqvl8h1dlrl7ylzy9mwsqc6wg5")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -4388,13 +6020,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.48.3") + (version "1.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1")))) + "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -4432,14 +6064,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz")))) + "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -4466,13 +6098,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.48.0") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn")))) + "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -4493,14 +6125,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm")))) + "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -4524,14 +6156,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g")))) + "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -4550,17 +6182,44 @@ testing and other simple calculations.") Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. Harshlight marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package +replaces the defected areas with @code{N/A}s or the median of the values of +the same probe. The new version handles the substitute value as a whole +matrix to solve the memory problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj")))) + "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -4573,14 +6232,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.28.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f")))) + "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -4602,13 +6261,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.70.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2")))) + "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -4622,14 +6281,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg")))) + "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -4647,14 +6306,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.36.3") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni")))) + "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -4671,13 +6330,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-lfa (package (name "r-lfa") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lfa" version)) (sha256 - (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l")))) + (base32 "0047wspvarbnbawrwvfjfz5y6i36l2r2k2501zjya09rjpiq101m")))) (properties `((upstream-name . "lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) @@ -4692,13 +6351,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.52.2") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65")))) + "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -4711,13 +6370,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-made4 (package (name "r-made4") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5")))) + "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -4737,16 +6396,111 @@ reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an Affymetrix +@acronym{CDF, chip description file} and creates a hash table environment +containing the location/probe set membership mapping. The other one creates a +package that automatically loads that environment.") + (license license:gpl2+))) + +(define-public r-maser + (package + (name "r-maser") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "maser" version)) + (sha256 + (base32 + "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv")))) + (properties `((upstream-name . "maser"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-dplyr + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-reshape2 + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/DiogoVeiga/maser") + (synopsis "Mapping alternative splicing events to proteins") + (description + "This package provides functionalities for downstream analysis, annotation +and visualizaton of alternative splicing events generated by rMATS.") + (license license:expat))) + +(define-public r-metaneighbor + (package + (name "r-metaneighbor") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MetaNeighbor" version)) + (sha256 + (base32 + "1gjjp5qlmv26sd3fvrd8cgv3invckxr8ldjpizpqm4mxjzifxwpm")))) + (properties `((upstream-name . "MetaNeighbor"))) + (build-system r-build-system) + (propagated-inputs + (list r-beanplot + r-dplyr + r-ggplot2 + r-gplots + r-igraph + r-matrix + r-matrixstats + r-rcolorbrewer + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MetaNeighbor") + (synopsis "Single cell replicability analysis") + (description + "This package implements a method to rapidly assess cell type identity using +both functional and random gene sets and it allows users to quantify cell type +replicability across datasets using neighbor voting. @code{MetaNeighbor} works +on the basis that cells of the same type should have more similar gene expression +profiles than cells of different types.") + (license license:expat))) + (define-public r-methylkit (package (name "r-methylkit") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35")))) + "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -4814,14 +6568,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd")))) + "07b1z8rd0zibmv3rm4zggjf49lh37p2bp1h919zcw3n0fy2hax1k")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -4864,14 +6618,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) + "071s1hfxln8zdr303g0ifmajd3kcfxxb6dds0pz67chc2gmgnd9q")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -4910,14 +6664,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.22.0") + (version "2.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) + "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -4955,14 +6709,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq")))) + "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -5012,14 +6766,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) + "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -5043,14 +6797,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) + "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -5091,17 +6845,84 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. It does not require +tumor/normal-paired DNA or genotype data, but operates solely on the donor +scRNA-data data (for example, 10x Cell Ranger output). It can be used to: + +@enumerate +@item detect allele-specific copy number variations from single-cells +@item differentiate tumor versus normal cells in the tumor microenvironment +@item infer the clonal architecture and evolutionary history of profiled tumors +@end enumerate + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -5133,14 +6954,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.38.1") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) + "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -5165,14 +6986,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) + "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -5220,14 +7041,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.88.0") + (version "1.90.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) + "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -5289,14 +7110,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05")))) + "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -5309,14 +7130,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y")))) + "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -5331,13 +7152,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf")))) + "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -5381,14 +7202,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f")))) + "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -5412,14 +7233,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) + "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -5462,13 +7283,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff")))) + "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) @@ -5489,14 +7310,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs")))) + "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs @@ -5515,13 +7336,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10")))) + "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -5580,13 +7401,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) + "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk")))) (build-system r-build-system) (arguments `(#:phases @@ -5659,13 +7480,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b")))) + (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -5696,13 +7517,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) + (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -5738,16 +7559,53 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scistreer + (package + (name "r-scistreer") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "scistreer" version)) + (sha256 + (base32 + "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) + (properties `((upstream-name . "scistreer"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-dplyr + r-ggplot2 + r-ggtree + r-igraph + r-paralleldist + r-patchwork + r-phangorn + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-reshape2 + r-rhpcblasctl + r-stringr + r-tidygraph)) + (home-page "https://github.com/kharchenkolab/scistreer") + (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") + (description + "This package provides fast maximum-likelihood phylogeny inference from +noisy single-cell data using the ScisTree algorithm proposed by +@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the +method applicable to massive single-cell datasets (>10,000 cells).") + (license license:gpl3))) + (define-public r-scmap (package (name "r-scmap") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) + (base32 "0rq185ynk874vgw4a5s2n92381dj6kxxnx2fcx2v7b2ahr3ybys7")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -5783,13 +7641,13 @@ different experiment.") (define-public r-scry (package (name "r-scry") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193")))) + "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs @@ -5815,14 +7673,14 @@ single-cell RNA-seq.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) + "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -5838,13 +7696,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn")))) + "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -5861,14 +7719,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.54.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq")))) + "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -5904,14 +7762,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) + "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -5945,13 +7803,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03")))) + (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -5995,14 +7853,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) + "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -6019,16 +7877,44 @@ 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-scds + (package + (name "r-scds") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scds" version)) + (sha256 + (base32 + "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + (properties `((upstream-name . "scds"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-matrix + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scds") + (synopsis "In-silico doublet annotation for single cell RNA sequencing data") + (description + "This is an R package for doublet annotation of single cell RNA +sequencing data. @code{scds} provides methods to annotate doublets in +scRNA-seq data computationally.") + (license license:expat))) + (define-public r-slingshot (package (name "r-slingshot") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2")))) + "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -6051,16 +7937,56 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +;; This is a CRAN package but it depends on a bioconductor package. +(define-public r-speaq + (package + (name "r-speaq") + (version "2.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "speaq" version)) + (sha256 + (base32 + "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) + (properties `((upstream-name . "speaq"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-data-table + r-dosnow + r-foreach + r-ggplot2 + r-gridextra + r-impute + r-massspecwavelet + r-missforest + r-reshape2 + r-rfast + r-rvest + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=speaq") + (synopsis "Tools for nuclear magnetic resonance spectra alignment") + (description + "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance} +spectroscopy data analysis as easy as possible. It only requires a small set +of functions to perform an entire analysis. Speaq offers the possibility of +raw spectra alignment and quantitation but also an analysis based on features +whereby the spectra are converted to peaks which are then grouped and turned +into features. These features can be processed with any number of statistical +tools either included in speaq or available elsewhere on CRAN.") + (license license:asl2.0))) + (define-public r-stager (package (name "r-stager") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y")))) + (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -6077,13 +8003,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.8.4") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379")))) + (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -6110,13 +8036,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6")))) + (base32 "11z3acsbaifrxkghd7i8503ki9s1lc6c22880yna6qcfprlzb44g")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -6147,13 +8073,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) + "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -6181,14 +8107,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4")))) + "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g")))) (build-system r-build-system) (propagated-inputs (list r-edger @@ -6212,14 +8138,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.2.2") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im")))) + "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -6255,13 +8181,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) + "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -6288,13 +8214,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) + "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -6313,17 +8239,18 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.6.5") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw")))) + "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph")))) (build-system r-build-system) (propagated-inputs (list r-broom + r-cli r-dplyr r-ggplot2 r-rcpp @@ -6345,13 +8272,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1")))) + "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -6383,14 +8310,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.64.0") + (version "3.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf")))) + "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -6452,13 +8379,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g")))) + (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -6488,13 +8415,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) + (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -6515,13 +8442,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.36.0") + (version "0.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk")))) + "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -6549,13 +8476,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv")))) + "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -6568,13 +8495,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz")))) + (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -6600,14 +8527,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc")))) + "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -6625,14 +8552,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk")))) + "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -6660,14 +8587,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy")))) + "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -6696,14 +8623,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw")))) + "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -6751,13 +8678,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby")))) + "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -6778,13 +8705,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg")))) + "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -6805,14 +8732,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.6.1") + (version "3.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr")))) + "039gy9ll6ingh3y5h2hp3rhbh2imaryjxzgf8ysk87irlbpnx1qs")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -6883,13 +8810,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg")))) + "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -6915,14 +8842,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82")))) + "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) @@ -6950,13 +8877,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4")))) + "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) @@ -7013,6 +8940,35 @@ classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) +(define-public r-pepsnmr + (package + (name "r-pepsnmr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "PepsNMR" version)) + (sha256 + (base32 + "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5")))) + (properties `((upstream-name . "PepsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-gridextra + r-matrix + r-matrixstats + r-ptw + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ManonMartin/PepsNMR") + (synopsis "Pre-process 1H-NMR FID signals") + (description + "This package provides R functions for common pre-processing steps that +are applied on @acronym{1H-NMR, proton nuclear magnetic resonance} data. It +also provides a function to read the @acronym{FID, free induction decay} +signals directly in the Bruker format.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package @@ -7043,14 +8999,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.30.1") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y")))) + "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -7097,13 +9053,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f")))) + "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -7124,12 +9080,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i")))) + (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -7143,12 +9099,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr")))) + (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -7162,12 +9118,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65")))) + (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -7181,12 +9137,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm")))) + (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -7213,14 +9169,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.30.0") + (version "2.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j")))) + "0lq2wfm3ibrpha9mqhhp6dgsx4jm2kwxvvrj0b62dzqspvg743wh")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -7237,14 +9193,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0")))) + "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -7271,14 +9227,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp")))) + "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -7312,14 +9268,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26")))) + "0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -7340,14 +9296,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5")))) + "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -7374,14 +9330,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx")))) + "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -7415,14 +9371,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb")))) + "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -7435,14 +9391,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48")))) + "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7461,14 +9417,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz")))) + "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -7491,17 +9447,52 @@ representations of analysis results in order to provide additional information.") (license license:lgpl3))) +(define-public r-glmgampoi + (package + (name "r-glmgampoi") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "glmGamPoi" version)) + (sha256 + (base32 + "1qxzbh5i208cpghmysailachj8xpx4g4iqk8552xjpjkn54pkpbd")))) + (properties `((upstream-name . "glmGamPoi"))) + (build-system r-build-system) + (propagated-inputs + (list r-beachmat + r-biocgenerics + r-delayedarray + r-delayedmatrixstats + r-hdf5array + r-matrixgenerics + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rlang + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/const-ae/glmGamPoi") + (synopsis "Fit a Gamma-Poisson Generalized Linear Model") + (description + "Fit linear models to overdispersed count data. The package can estimate +the overdispersion and fit repeated models for matrix input. It is designed +to handle large input datasets as they typically occur in single cell RNA-seq +experiments.") + (license license:gpl3))) + (define-public r-rots (package (name "r-rots") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r")))) + "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -7517,14 +9508,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77")))) + "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -7541,14 +9532,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax")))) + "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -7587,14 +9578,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6")))) + "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -7614,14 +9605,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x")))) + "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -7639,14 +9630,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x")))) + "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -7667,14 +9658,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl")))) + "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -7693,14 +9684,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla")))) + "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -7722,22 +9713,56 @@ heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.") (license license:artistic2.0))) +(define-public r-treesummarizedexperiment + (package + (name "r-treesummarizedexperiment") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "TreeSummarizedExperiment" version)) + (sha256 + (base32 + "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2")))) + (properties `((upstream-name . "TreeSummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-dplyr + r-iranges + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-treeio)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TreeSummarizedExperiment") + (synopsis "S4 class for data with tree structures") + (description + "@code{TreeSummarizedExperiment} extends @code{SingleCellExperiment} to +include hierarchical information on the rows or columns of the rectangular +data.") + (license license:gpl2+))) + (define-public r-ggtree (package (name "r-ggtree") - (version "3.4.0") + (version "3.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4")))) + "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs (list r-ape r-aplot + r-cli r-dplyr r-ggfun r-ggplot2 @@ -7762,14 +9787,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b")))) + "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -7791,14 +9816,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x")))) + "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -7826,14 +9851,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.10.0") + (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy")))) + "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -7870,14 +9895,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k")))) + "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -7892,14 +9917,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz")))) + "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -7932,13 +9957,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd")))) + "1a664bllaq9pbb5cpd01j919qirylvnm8qd49lwlz89jvqjdri19")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) @@ -7952,14 +9977,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.70.0") + (version "1.72.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc")))) + "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -8050,14 +10075,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) + "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -8072,13 +10097,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk")))) + "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -8110,14 +10135,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.24.0") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) + "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3")))) (build-system r-build-system) (arguments (list @@ -8149,14 +10174,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) + "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -8178,14 +10203,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) + "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -8215,14 +10240,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4")))) + "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -8244,14 +10269,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.12.3") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc")))) + "1yj84ba6px14hbqg8526527vfcxmzvmly34f7hba4vybdm1jscfm")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -8287,14 +10312,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi")))) + "133ijkw5sd0gl38dfr7qfqvvp2df7lg6j8vkvy54zlpamkg6l2x1")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -8322,14 +10347,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.24.1") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn")))) + "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -8507,14 +10532,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27")))) + "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -8533,14 +10558,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0")))) + "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -8571,14 +10596,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851")))) + "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -8615,14 +10640,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.64.2") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x")))) + "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -8650,14 +10675,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62")))) + "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -8671,14 +10696,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l")))) + "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -8695,14 +10720,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw")))) + "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -8726,16 +10751,101 @@ to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) +(define-public r-mia + (package + (name "r-mia") + (version "1.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "mia" version)) + (sha256 + (base32 + "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync")))) + (properties `((upstream-name . "mia"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocparallel + r-biostrings + r-decipher + r-decontam + r-delayedarray + r-delayedmatrixstats + r-dirichletmultinomial + r-dplyr + r-iranges + r-mass + r-multiassayexperiment + r-rlang + r-s4vectors + r-scater + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-tidyr + r-treesummarizedexperiment + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/microbiome/mia") + (synopsis "Microbiome analysis") + (description + "The mia package implements tools for microbiome analysis based on the +@code{SummarizedExperiment}, @code{SingleCellExperiment} and +@code{TreeSummarizedExperiment} infrastructure. Data wrangling and analysis +in the context of taxonomic data is the main scope. Additional functions for +common task are implemented such as community indices calculation and +summarization.") + (license license:artistic2.0))) + +(define-public r-microbiome + (package + (name "r-microbiome") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "microbiome" version)) + (sha256 + (base32 + "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x")))) + (properties `((upstream-name . "microbiome"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-compositions + r-dplyr + r-ggplot2 + r-phyloseq + r-reshape2 + r-rtsne + r-scales + r-tibble + r-tidyr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://microbiome.github.io/microbiome/") + (synopsis "Tools for microbiome analysis") + (description + "This package facilitates phyloseq exploration and analysis of taxonomic +profiling data. This package provides tools for the manipulation, statistical +analysis, and visualization of taxonomic profiling data. In addition to +targeted case-control studies, microbiome facilitates scalable exploration of +population cohorts. This package supports the independent phyloseq data +format and expands the available toolkit in order to facilitate the +standardization of the analyses and the development of best practices.") + (license license:bsd-2))) + (define-public r-milor (package (name "r-milor") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs")))) + "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -8777,14 +10887,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6")))) + "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -8828,14 +10938,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww")))) + "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -8875,14 +10985,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d")))) + "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -8914,14 +11024,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.20.0") + (version "2.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb")))) + "16d7viyidqbsy3mbr2cpq9p291yf362a4blhvs05qxcwm3fjllij")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -8975,14 +11085,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi")))) + "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -9071,13 +11181,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0")))) + "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -9140,14 +11250,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix")))) + "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -9180,14 +11290,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.4.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1")))) + "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -9205,14 +11315,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd")))) + "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -9232,14 +11342,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c")))) + "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -9262,14 +11372,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.64.0") + (version "1.66.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif")))) + "1ln1n4zwmjw1ils45vix93q3h19xlg4q894yhhxkphgyj0qcy00b")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -9284,13 +11394,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp")))) + (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -9317,22 +11427,22 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg")))) + "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel + r-cowplot r-data-table r-fastmatch r-ggplot2 - r-gridextra r-matrix r-rcpp)) (native-inputs @@ -9349,23 +11459,23 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.22.0") + (version "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp")))) + "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel - r-do-db r-fgsea r-ggplot2 r-gosemsim + r-hdo-db r-qvalue r-reshape2)) (native-inputs @@ -9384,20 +11494,21 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.16.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02")))) + "0nzcr23m58z3h0n0frxf26z14j7ilcl4fjy7rqm7f2i1wyld70zl")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggplot2 r-ggraph + r-ggnewscale r-ggtree r-gosemsim r-igraph @@ -9406,6 +11517,7 @@ data.") r-purrr r-rcolorbrewer r-reshape2 + r-rlang r-scatterpie r-shadowtext r-yulab-utils)) @@ -9422,14 +11534,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.4") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5")))) + "0fm2cz2464xh075p4yl6bha9m6didc41ng4a3flkw1f1cvvpi4g0")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -9441,6 +11553,7 @@ All the visualization methods are developed based on ggplot2 graphics.") r-enrichplot r-go-db r-gosemsim + r-gson r-magrittr r-plyr r-qvalue @@ -9459,13 +11572,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.16.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f")))) + "1f3f56d88yiqyj45rhcwqb04wbxr9m4fxhbbckw1j7nykm8100ps")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9505,14 +11618,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5")))) + "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -9535,6 +11648,7 @@ expression data sets.") r-rpart r-sfsmisc r-shiny + r-summarizedexperiment r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") @@ -9547,14 +11661,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq")))) + "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg")))) (build-system r-build-system) (arguments `(#:phases @@ -9579,14 +11693,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390")))) + "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -9603,14 +11717,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw")))) + "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -9633,14 +11747,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9")))) + "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -9657,14 +11771,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0")))) + "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -9681,14 +11795,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn")))) + "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -9712,14 +11826,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r")))) + "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -9733,14 +11847,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b")))) + "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -9781,14 +11895,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8")))) + "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -9806,14 +11920,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4")))) + "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -9860,12 +11974,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi")))) + (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -9887,12 +12001,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg")))) + (base32 "0lq79as9gb48hf3v2xj895s0nsjr37fqah4p405kdybzry56gvrq")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -9937,14 +12051,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z")))) + "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -9969,14 +12083,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.8.2") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j")))) + "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -10007,14 +12121,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp")))) + "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -10054,14 +12168,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk")))) + "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -10159,14 +12273,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51")))) + "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -10184,14 +12298,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z")))) + "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -10227,14 +12341,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.18.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr")))) + "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -10243,6 +12357,7 @@ investigation using RNA-seq data.") r-delayedarray r-delayedmatrixstats r-gseabase + r-matrix r-mixtools r-r-utils r-shiny @@ -10267,14 +12382,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.38.0") + (version "4.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si")))) + "1k6gbivwlai451whq2vr3c0shzs9p4g188jn5waw7973gdzdi00q")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -10306,14 +12421,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8")))) + "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10339,14 +12454,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff")))) + "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -10365,14 +12480,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6")))) + "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -10404,14 +12519,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid")))) + "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -10453,14 +12568,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.68.0") + (version "2.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d")))) + "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -10535,14 +12650,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3")))) + "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10568,14 +12683,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg")))) + "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10605,14 +12720,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc")))) + "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10673,14 +12788,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39")))) + "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -10697,14 +12812,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.18.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm")))) + "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10738,13 +12853,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f")))) + "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -10779,14 +12894,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca")))) + "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -10803,14 +12918,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i")))) + "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -10837,14 +12952,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d")))) + "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -10858,14 +12973,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah")))) + "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -10890,14 +13005,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i")))) + "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -10923,14 +13038,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji")))) + "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -10948,14 +13063,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg")))) + "05cczwkhv7kfnhlr0qznk6vdjncaj907895923f8mwx4j4cy5gcz")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -10975,14 +13090,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b")))) + "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11007,14 +13122,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1")))) + "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -11030,14 +13145,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw")))) + "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -11063,14 +13178,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.32.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm")))) + "05y4jmbf8sxl32f3g5lw9ycxky0rw69gax3n2z0kif7xcb5qf3qv")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -11093,14 +13208,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q")))) + "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -11129,14 +13244,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp")))) + "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -11172,14 +13287,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7")))) + "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -11210,14 +13325,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) + "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -11252,14 +13367,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) + "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -11295,14 +13410,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) + "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -11348,14 +13463,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) + "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -11385,19 +13500,21 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.28.2") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) + "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb")))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-ggplot2 r-multiassayexperiment r-multidataset + r-plotly r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes @@ -11425,14 +13542,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.24.2") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) + "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11460,14 +13577,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) + "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -11501,14 +13618,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.4") + (version "2.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl")))) + "1gvd8vmglvzc3bixqxrm4k7yikl2as5l4x6bvvvnwsgx2i7vz7dm")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -11553,14 +13670,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) + "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -11619,14 +13736,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg")))) + "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -11648,24 +13765,24 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr")))) + "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-matrixstats r-rcpp - r-rcpparmadillo r-rprotobuflib r-s4vectors)) (native-inputs @@ -11680,14 +13797,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y")))) + "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -11703,14 +13820,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m")))) + "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -11734,14 +13851,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.24.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359")))) + "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -11771,14 +13888,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f")))) + "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -11802,14 +13919,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.34.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) + "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -11836,14 +13953,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp")))) + "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -11865,38 +13982,31 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.8.0") + (version "4.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss")))) + "0jmbfclkfm0n2mshk94906kivii7awlskf7l7ydn8ki8wrpzxqg4")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - (list r-aws-s3 - r-aws-signature - r-bh + (list r-bh r-biobase r-biocgenerics + r-cpp11 r-cytolib r-data-table r-delayedarray - r-digest r-dplyr r-flowcore r-ggplot2 r-graph - r-lattice - r-latticeextra r-matrixstats r-ncdfflow r-rbgl - r-rcpp - r-rcpparmadillo - r-rcppparallel r-rgraphviz r-rhdf5lib r-rprotobuflib @@ -11919,14 +14029,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.8.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) + "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -11957,38 +14067,30 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.8.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) + "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-bh + r-biobase r-biocgenerics - r-clue + r-cpp11 r-data-table r-flowclust r-flowcore - r-flowstats r-flowviz r-flowworkspace r-graph - r-gtools - r-ks - r-lattice - r-mass r-ncdfflow - r-plyr - r-r-utils r-rbgl - r-rcolorbrewer - r-rcpp - r-rrcov)) + r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") @@ -12001,14 +14103,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr")))) + "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -12053,14 +14155,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) + "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -12096,14 +14198,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.20.0") + (version "6.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) + "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -12142,14 +14244,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) + "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -12188,14 +14290,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.16.0") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) + "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -12230,14 +14332,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) + "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -12276,14 +14378,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5")))) + "0grzp9k06dz04bw07nf9qka19mara1kplyd24y8mg8208wk949f6")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -12343,14 +14445,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) + "07l8vaqbw36hvs8pyn1gk6dglnmkcmbafvd4rdrhg2wqwnlpsf40")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -12478,14 +14580,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l")))) + "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -12502,14 +14604,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2")))) + "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -12524,14 +14626,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv")))) + "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -12562,14 +14664,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0")) + "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -12618,14 +14720,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) + "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -12649,14 +14751,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) + "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -12673,14 +14775,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r")))) + "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -12696,14 +14798,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6")))) + "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -12784,14 +14886,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8")))) + "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -12890,14 +14992,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv")))) + "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -12918,6 +15020,7 @@ arrays based on fast wavelet-based functional models.") r-pbkrtest r-progress r-rdpack + r-remacor r-reshape2 r-rhpcblasctl r-rlang @@ -12938,14 +15041,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc")))) + "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -12968,14 +15071,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh")))) + "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -12992,14 +15095,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr")))) + "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -13040,13 +15143,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m")))) + "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -13069,13 +15172,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d")))) + "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -13093,13 +15196,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25")))) + "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -13120,13 +15223,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2")))) + "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -13213,14 +15316,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj")))) + "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -13235,14 +15338,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) + "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -13271,14 +15374,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5")))) + "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -13297,14 +15400,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2")))) + "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -13319,14 +15422,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq")))) + "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -13348,14 +15451,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v")))) + "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -13374,14 +15477,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp")))) + "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -13396,14 +15499,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6")))) + "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -13418,14 +15521,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw")))) + "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -13482,14 +15585,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj")))) + "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -13525,14 +15628,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.48.0") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma")))) + "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -13568,13 +15671,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30")))) + (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -13597,14 +15700,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz")))) + "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -13632,14 +15735,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh")))) + "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -13661,18 +15764,18 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g")))) + "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang)) + (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -13684,14 +15787,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5")))) + "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -13701,6 +15804,7 @@ symbols).") r-ggplot2 r-ggraph r-graphite + r-gson r-igraph r-reactome-db)) (native-inputs @@ -13716,14 +15820,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk")))) + "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -13735,6 +15839,28 @@ enrichment analysis and several functions for visualization.") microarray data.") (license license:gpl2+))) +(define-public r-biocbaseutils + (package + (name "r-biocbaseutils") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocBaseUtils" version)) + (sha256 + (base32 + "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69")))) + (properties `((upstream-name . "BiocBaseUtils"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BiocBaseUtils") + (synopsis "General utility functions for developing Bioconductor packages") + (description + "The package provides utility functions related to package development. +These include functions that replace slots, and selectors for show methods. +It aims to coalesce the various helper functions often re-used throughout the +Bioconductor ecosystem.") + (license license:artistic2.0))) + (define-public r-bioccasestudies (package (name "r-bioccasestudies") @@ -13760,13 +15886,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.32.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc")))) + "1zj43kbzvi2ws8c182fp6vn5r6iiqsr6p2iyy3k8n3ifm2acqw2h")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -13789,14 +15915,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn")))) + "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -13811,13 +15937,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5")))) + "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -13835,13 +15961,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.64.0") + (version "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126")))) + "0fdxlixwf4d3p1prq37cgfvaiym44h2yd4bym6wp4dl8h648v99y")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -13853,6 +15979,7 @@ functionality.") r-rcurl r-xml r-runit)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -13863,14 +15990,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl")))) + "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -13897,14 +16024,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai")))) + "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -13924,20 +16051,22 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1")))) + "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-biocbaseutils r-biocgenerics + r-delayedarray r-genomicranges r-iranges r-s4vectors @@ -13959,14 +16088,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi")))) + "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -14004,14 +16133,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3")))) + "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -14031,14 +16160,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h")))) + "1av7vnw6z9cw7j4d3vpi8mfs5h4pn4yr2wc8ybg7ad1d686ah845")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -14058,11 +16187,10 @@ gene selection, testing relationships, and so on.") r-rbgl r-readr r-rlang + r-rorcid r-rvest r-stringr r-tibble - r-tidyr - r-tidyselect r-xml2)) (native-inputs (list r-knitr)) @@ -14079,14 +16207,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh")))) + "1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -14117,14 +16245,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l")))) + "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -14150,14 +16278,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0")))) + "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -14172,14 +16300,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v")))) + "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -14218,18 +16346,40 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.28.0") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky")))) + "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (list r-annotationdbi + r-circlize + r-digest + r-doparallel + r-dt + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-getoptlong + r-globaloptions + r-go-db + r-iranges + r-org-hs-eg-db + r-progress + r-rcolorbrewer + r-rcurl + r-rcpp + r-rjson + r-s4vectors + r-shiny + r-txdb-hsapiens-ucsc-hg19-knowngene + r-txdb-hsapiens-ucsc-hg38-knowngene)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") @@ -14242,14 +16392,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012")))) + "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -14275,14 +16425,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc")))) + "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -14398,14 +16548,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.58.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf")))) + "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -14419,13 +16569,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.34.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k")))) + "16lssnmhy3klqp4sw1328f38cixkjh9317gdyikcrmsbcwg2ak6v")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -14486,14 +16636,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l")))) + "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -14521,16 +16671,54 @@ data manipulation and visualization.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fishpond + (package + (name "r-fishpond") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "fishpond" version)) + (sha256 + (base32 + "112jd53wbiv1w0n8dc4qn6257wbbbg5i20s9wlvaw98jma94afa6")))) + (properties `((upstream-name . "fishpond"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-abind + r-genomicranges + r-gtools + r-iranges + r-jsonlite + r-matrix + r-matrixstats + r-qvalue + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-svmisc)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/fishpond") + (synopsis "Downstream methods and tools for expression data") + (description + "The @code{fishpond} package contains methods for differential transcript +and gene expression analysis of RNA-seq data using inferential replicates for +uncertainty of abundance quantification, as generated by Gibbs sampling or +bootstrap sampling. Also the package contains a number of utilities for +working with Salmon and Alevin quantification files.") + (license license:gpl2))) + (define-public r-fithic (package (name "r-fithic") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq")))) + "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -14548,13 +16736,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s")))) + "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -14577,14 +16765,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday")))) + "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -14608,14 +16796,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g")) + "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7")) (modules '((guix build utils))) (snippet '(begin @@ -14688,14 +16876,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c")))) + "0sa1wh997jfiz2y0dr7v12b7pvlf7icgv6arlyqy57winbnqa96m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) @@ -14714,13 +16902,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq")))) + (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -14762,14 +16950,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w")))) + "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -14808,13 +16996,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6")))) + (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs @@ -14837,14 +17025,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878")))) + "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -14871,13 +17059,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.18.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m")))) + (base32 "1nhhpqhpvmw6b0nwxdwsjnakmfpxzpii8fmabwwg9bk8ni3zj5dq")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -14918,14 +17106,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p")))) + "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -14946,13 +17134,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.10.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y")))) + (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -14978,14 +17166,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.6.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn")))) + "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -15013,13 +17201,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw")))) + "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -15032,8 +17220,10 @@ of other packages.") r-ggbeeswarm r-ggplot2 r-ggrepel + r-ggrastr r-gridextra r-matrix + r-pheatmap r-rcolorbrewer r-rcppml r-rlang @@ -15042,6 +17232,7 @@ of other packages.") r-scuttle r-singlecellexperiment r-summarizedexperiment + r-uwot r-viridis)) (native-inputs (list r-knitr)) @@ -15055,14 +17246,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.24.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w")))) + "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -15098,14 +17289,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2")))) + "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -15123,14 +17314,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv")))) + "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -15159,14 +17350,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh")))) + "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -15188,13 +17379,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3")))) + (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -15218,14 +17409,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp")))) + "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -15251,14 +17442,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42")))) + "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -15274,14 +17465,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi")))) + "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -15303,14 +17494,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza")))) + "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -15366,14 +17557,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b")))) + "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -15406,14 +17597,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg")))) + "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g")))) (build-system r-build-system) (arguments `(#:phases @@ -15574,14 +17765,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi")))) + "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -15623,14 +17814,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.28.1") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl")))) + "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -15657,13 +17848,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.56.0") + (version "1.58.3") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx")))) + (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -15681,14 +17872,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm")))) + "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -15805,13 +17996,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq")))) + (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -15839,14 +18030,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2")))) + "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -15863,14 +18054,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7")))) + "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -15901,14 +18092,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh")))) + "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -15954,14 +18145,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708")))) + "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -15988,14 +18179,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8")))) + "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -16021,14 +18212,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15")))) + "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -16037,6 +18228,7 @@ regions or annotations of your choice from BigWig files.") r-data-table r-dixontest r-futile-logger + r-ids r-matrix r-rcpp r-rdpack)) @@ -16054,14 +18246,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh")))) + "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -16090,14 +18282,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.22.3") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k")))) + "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -16124,14 +18316,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa")))) + "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -16148,14 +18340,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.54.0") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam")))) + "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -16170,14 +18362,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70")))) + "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -16195,14 +18387,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq")))) + "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -16219,14 +18411,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk")))) + "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -16243,14 +18435,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.8.0") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh")))) + "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -16269,14 +18461,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0")))) + "0zmiaixknwxv72l4fygrn0qr3mvl7kqfbqgflnavs0wxx6xdjqgn")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -16303,14 +18495,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6")))) + "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -16333,14 +18525,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.4.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni")))) + "0mbqsias2ajw29d1wgl10y2cjqv3slrsgifccz0kh9l5r6bk28vz")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -16378,14 +18570,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n")))) + "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -16407,14 +18599,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g")))) + "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -16427,14 +18619,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz")))) + "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -16449,14 +18641,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln")))) + "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs @@ -16474,32 +18666,32 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj")))) + "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-complexheatmap - r-deseq2 r-dynamictreecut r-genie3 r-ggnetwork r-ggnewscale r-ggplot2 - r-ggpubr + r-ggrepel r-igraph r-intergraph r-matrixstats r-minet r-netrep r-networkd3 + r-patchwork r-rcolorbrewer r-reshape2 r-summarizedexperiment @@ -16530,14 +18722,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm")))) + "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -16559,14 +18751,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2")))) + "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs @@ -16601,14 +18793,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m")))) + "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -16627,14 +18819,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6")))) + "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -16657,14 +18849,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22")))) + "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -16699,14 +18891,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5")))) + "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -16742,17 +18934,54 @@ ensemble machine learning for the estimation of nuisance functions.") visualizing bisulfite sequencing data.") (license license:artistic2.0))) +(define-public r-dada2 + (package + (name "r-dada2") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dada2" version)) + (sha256 + (base32 + "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc")))) + (properties `((upstream-name . "dada2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-rcpp + r-rcppparallel + r-reshape2 + r-shortread + r-xvector)) + (native-inputs (list r-knitr)) + (home-page "https://benjjneb.github.io/dada2/") + (synopsis + "Accurate, high-resolution sample inference from amplicon sequencing data") + (description + "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs) +from high-throughput amplicon sequencing data, replacing the coarser and less +accurate OTU clustering approach. The dada2 pipeline takes as input +demultiplexed fastq files, and outputs the sequence variants and their +sample-wise abundances after removing substitution and chimera errors. +Taxonomic classification is available via a native implementation of the RDP +naive Bayesian classifier, and species-level assignment to 16S rRNA gene +fragments by exact matching.") + (license license:lgpl2.0))) + (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n")))) + "1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -16791,13 +19020,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj")))) + "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -16810,13 +19039,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.4.0") + (version "3.5.25") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni")))) + (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -16836,12 +19065,14 @@ interest on transformed methylation proportions.") r-later r-logger r-magrittr + r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang + r-rvest r-stringr r-tibble r-tidyr @@ -16863,14 +19094,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr")))) + "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -16915,13 +19146,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.24.3") + (version "2.25.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms")))) + (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -16970,13 +19201,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln")))) + "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -17009,14 +19240,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl")))) + "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -17050,13 +19281,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k")))) + (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs |