From 80eb01c7763e99603dac6c1e4ad41f521fed5c26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 14:34:41 +0100 Subject: gnu: r-gkmsvm: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here... * gnu/packages/bioconductor.scm (r-gkmsvm): ...to here. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 710b9fd07a..f687a03030 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2521,3 +2521,37 @@ summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-gkmsvm + (package + (name "r-gkmsvm") + (version "0.79.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "gkmSVM" version)) + (sha256 + (base32 + "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) + (properties `((upstream-name . "gkmSVM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernlab" ,r-kernlab) + ("r-rcpp" ,r-rcpp) + ("r-rocr" ,r-rocr) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr))) + (home-page "https://cran.r-project.org/web/packages/gkmSVM") + (synopsis "Gapped-kmer support vector machine") + (description + "This R package provides tools for training gapped-kmer SVM classifiers +for DNA and protein sequences. This package supports several sequence +kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") + (license license:gpl2+))) -- cgit v1.2.3 From 8a5460b4fb32962e835ec08907210f6416e53582 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:09:07 +0100 Subject: gnu: Add r-triform. * gnu/packages/bioconductor.scm (r-triform): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f687a03030..7bd126b5c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2555,3 +2555,27 @@ surface of a flowcell.") for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) + +(define-public r-triform + (package + (name "r-triform") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "triform" version)) + (sha256 + (base32 + "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-yaml" ,r-yaml))) + (home-page "https://bioconductor.org/packages/triform/") + (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") + (description + "The Triform algorithm uses model-free statistics to identify peak-like +distributions of TF ChIP sequencing reads, taking advantage of an improved +peak definition in combination with known profile characteristics.") + (license license:gpl2))) -- cgit v1.2.3 From c538bcdd38ca12fbdf02b220a371ac16448cab8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:09:16 +0100 Subject: gnu: Add r-varianttools. * gnu/packages/bioconductor.scm (r-varianttools): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7bd126b5c0..744fc8780d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2579,3 +2579,43 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.") (license license:gpl2))) + +(define-public r-varianttools + (package + (name "r-varianttools") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "VariantTools" version)) + (sha256 + (base32 + "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j")))) + (properties `((upstream-name . "VariantTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/VariantTools/") + (synopsis "Tools for exploratory analysis of variant calls") + (description + "Explore, diagnose, and compare variant calls using filters. The +VariantTools package supports a workflow for loading data, calling single +sample variants and tumor-specific somatic mutations or other sample-specific +variant types (e.g., RNA editing). Most of the functions operate on +alignments (BAM files) or datasets of called variants. The user is expected +to have already aligned the reads with a separate tool, e.g., GSNAP via +gmapR.") + (license license:artistic2.0))) -- cgit v1.2.3 From 3e41919d5123ec7a5772ec2828a157ec64cfb947 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:19:40 +0100 Subject: gnu: Add r-heatplus. * gnu/packages/bioconductor.scm (r-heatplus): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 744fc8780d..a17372da82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2619,3 +2619,28 @@ alignments (BAM files) or datasets of called variants. The user is expected to have already aligned the reads with a separate tool, e.g., GSNAP via gmapR.") (license license:artistic2.0))) + +(define-public r-heatplus + (package + (name "r-heatplus") + (version "2.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Heatplus" version)) + (sha256 + (base32 + "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48")))) + (properties `((upstream-name . "Heatplus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://github.com/alexploner/Heatplus") + (synopsis "Heatmaps with row and/or column covariates and colored clusters") + (description + "This package provides tools to display a rectangular heatmap (intensity +plot) of a data matrix. By default, both samples (columns) and features (row) +of the matrix are sorted according to a hierarchical clustering, and the +corresponding dendrogram is plotted. Optionally, panels with additional +information about samples and features can be added to the plot.") + (license license:gpl2+))) -- cgit v1.2.3 From c04f230eb3199b3b516584e102a87fc0e456806a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:19:52 +0100 Subject: gnu: Add r-gosemsim. * gnu/packages/bioconductor.scm (r-gosemsim): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a17372da82..78af3f5153 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2644,3 +2644,30 @@ of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.") (license license:gpl2+))) + +(define-public r-gosemsim + (package + (name "r-gosemsim") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOSemSim" version)) + (sha256 + (base32 + "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib")))) + (properties `((upstream-name . "GOSemSim"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-rcpp" ,r-rcpp))) + (home-page "https://guangchuangyu.github.io/software/GOSemSim") + (synopsis "GO-terms semantic similarity measures") + (description + "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide +quantitative ways to compute similarities between genes and gene groups, and +have became important basis for many bioinformatics analysis approaches. +GOSemSim is an R package for semantic similarity computation among GO terms, +sets of GO terms, gene products and gene clusters.") + (license license:artistic2.0))) -- cgit v1.2.3 From 9d0f794229faeb24801d30f20c5df47bc4a03041 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:20:00 +0100 Subject: gnu: Add r-anota. * gnu/packages/bioconductor.scm (r-anota): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78af3f5153..656a594d96 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2671,3 +2671,34 @@ have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.") (license license:artistic2.0))) + +(define-public r-anota + (package + (name "r-anota") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "anota" version)) + (sha256 + (base32 + "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0")))) + (build-system r-build-system) + (propagated-inputs + `(("r-multtest" ,r-multtest) + ("r-qvalue" ,r-qvalue))) + (home-page "https://bioconductor.org/packages/anota/") + (synopsis "Analysis of translational activity") + (description + "Genome wide studies of translational control is emerging as a tool to +study verious biological conditions. The output from such analysis is both +the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively +involved in translation (the actively translating mRNA level) for each mRNA. +The standard analysis of such data strives towards identifying differential +translational between two or more sample classes - i.e. differences in +actively translated mRNA levels that are independent of underlying differences +in cytosolic mRNA levels. This package allows for such analysis using partial +variances and the random variance model. As 10s of thousands of mRNAs are +analyzed in parallell the library performs a number of tests to assure that +the data set is suitable for such analysis.") + (license license:gpl3))) -- cgit v1.2.3 From a6d867fed9d54f8fe650be45ffb781b16f26dc7a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 25 Mar 2019 16:20:04 +0100 Subject: gnu: Add r-sigpathway. * gnu/packages/bioconductor.scm (r-sigpathway): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 656a594d96..59ca93dde8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2702,3 +2702,25 @@ variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) + +(define-public r-sigpathway + (package + (name "r-sigpathway") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sigPathway" version)) + (sha256 + (base32 + "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3")))) + (properties `((upstream-name . "sigPathway"))) + (build-system r-build-system) + (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") + (synopsis "Pathway analysis") + (description + "This package is used to conduct pathway analysis by calculating the NT_k +and NE_k statistics in a statistical framework for determining whether a +specified group of genes for a pathway has a coordinated association with a +phenotype of interest.") + (license license:gpl2))) -- cgit v1.2.3 From af26c7ae7010d72c8f4759f3f4e2421cd9a2183b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Mar 2019 15:24:14 +0100 Subject: gnu: Add r-fgsea. * gnu/packages/bioconductor.scm (r-fgsea): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 59ca93dde8..3f5e61f6f5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2724,3 +2724,32 @@ and NE_k statistics in a statistical framework for determining whether a specified group of genes for a pathway has a coordinated association with a phenotype of interest.") (license license:gpl2))) + +(define-public r-fgsea + (package + (name "r-fgsea") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fgsea" version)) + (sha256 + (base32 + "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-data-table" ,r-data-table) + ("r-fastmatch" ,r-fastmatch) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/ctlab/fgsea/") + (synopsis "Fast gene set enrichment analysis") + (description + "The package implements an algorithm for fast gene set enrichment +analysis. Using the fast algorithm allows to make more permutations and get +more fine grained p-values, which allows to use accurate stantard approaches +to multiple hypothesis correction.") + (license license:expat))) -- cgit v1.2.3 From f8a5af4653077502a3818b4c71ad7bf1be67389a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Mar 2019 15:43:37 +0100 Subject: gnu: Add r-do-db. * gnu/packages/bioconductor.scm (r-do-db): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f5e61f6f5..86c15c08ea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -708,6 +708,32 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +(define-public r-do-db + (package + (name "r-do-db") + (version "2.9") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "DO.db_" version ".tar.gz")) + (sha256 + (base32 + "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) + (properties + `((upstream-name . "DO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://www.bioconductor.org/packages/DO.db/") + (synopsis "Annotation maps describing the entire Disease Ontology") + (description + "This package provides a set of annotation maps describing the entire +Disease Ontology.") + (license license:artistic2.0))) + ;;; Experiment data -- cgit v1.2.3 From 305050b56d5df003f986cbca5fedb4b9b5cd45bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Mar 2019 15:45:20 +0100 Subject: gnu: Add r-dose. * gnu/packages/bioconductor.scm (r-dose): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 86c15c08ea..0c7be1c7d5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2779,3 +2779,37 @@ analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.") (license license:expat))) + +(define-public r-dose + (package + (name "r-dose") + (version "3.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DOSE" version)) + (sha256 + (base32 + "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa")))) + (properties `((upstream-name . "DOSE"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocparallel" ,r-biocparallel) + ("r-do-db" ,r-do-db) + ("r-fgsea" ,r-fgsea) + ("r-ggplot2" ,r-ggplot2) + ("r-gosemsim" ,r-gosemsim) + ("r-qvalue" ,r-qvalue) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://guangchuangyu.github.io/software/DOSE/") + (synopsis "Disease ontology semantic and enrichment analysis") + (description + "This package implements five methods proposed by Resnik, Schlicker, +Jiang, Lin and Wang, respectively, for measuring semantic similarities among +@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses +including hypergeometric model and gene set enrichment analysis are also +implemented for discovering disease associations of high-throughput biological +data.") + (license license:artistic2.0))) -- cgit v1.2.3 From 9c30cf65d2b2f1f529f9e7dc4ea58e14b3035f9e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Mar 2019 15:45:30 +0100 Subject: gnu: Add r-enrichplot. * gnu/packages/bioconductor.scm (r-enrichplot): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c7be1c7d5..098cee8100 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2813,3 +2813,39 @@ including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.") (license license:artistic2.0))) + +(define-public r-enrichplot + (package + (name "r-enrichplot") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "enrichplot" version)) + (sha256 + (base32 + "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-cowplot" ,r-cowplot) + ("r-dose" ,r-dose) + ("r-europepmc" ,r-europepmc) + ("r-ggplot2" ,r-ggplot2) + ("r-ggplotify" ,r-ggplotify) + ("r-ggraph" ,r-ggraph) + ("r-ggridges" ,r-ggridges) + ("r-gosemsim" ,r-gosemsim) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-upsetr" ,r-upsetr))) + (home-page "https://github.com/GuangchuangYu/enrichplot") + (synopsis "Visualization of functional enrichment result") + (description + "The enrichplot package implements several visualization methods for +interpreting functional enrichment results obtained from ORA or GSEA analyses. +All the visualization methods are developed based on ggplot2 graphics.") + (license license:artistic2.0))) -- cgit v1.2.3 From f8295ee6dea95eec54196c967f034a1597e45e70 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Mar 2019 15:45:35 +0100 Subject: gnu: Add r-clusterprofiler. * gnu/packages/bioconductor.scm (r-clusterprofiler): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 098cee8100..46d1880ccb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2849,3 +2849,36 @@ data.") interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics.") (license license:artistic2.0))) + +(define-public r-clusterprofiler + (package + (name "r-clusterprofiler") + (version "3.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "clusterProfiler" version)) + (sha256 + (base32 + "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm")))) + (properties + `((upstream-name . "clusterProfiler"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dose" ,r-dose) + ("r-enrichplot" ,r-enrichplot) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gosemsim" ,r-gosemsim) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-qvalue" ,r-qvalue) + ("r-rvcheck" ,r-rvcheck) + ("r-tidyr" ,r-tidyr))) + (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") + (synopsis "Analysis and visualization of functional profiles for gene clusters") + (description + "This package implements methods to analyze and visualize functional +profiles (GO and KEGG) of gene and gene clusters.") + (license license:artistic2.0))) -- cgit v1.2.3 From ce77562a9e8cf2280a87b5462c33affc06c98de6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:21:59 +0100 Subject: gnu: Add r-mlinterfaces. * gnu/packages/bioconductor.scm (r-mlinterfaces): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 46d1880ccb..26ebb0930b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2882,3 +2882,44 @@ All the visualization methods are developed based on ggplot2 graphics.") "This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.") (license license:artistic2.0))) + +(define-public r-mlinterfaces + (package + (name "r-mlinterfaces") + (version "1.62.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MLInterfaces" version)) + (sha256 + (base32 + "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8")))) + (properties `((upstream-name . "MLInterfaces"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cluster" ,r-cluster) + ("r-fpc" ,r-fpc) + ("r-gbm" ,r-gbm) + ("r-gdata" ,r-gdata) + ("r-genefilter" ,r-genefilter) + ("r-ggvis" ,r-ggvis) + ("r-hwriter" ,r-hwriter) + ("r-mass" ,r-mass) + ("r-mlbench" ,r-mlbench) + ("r-pls" ,r-pls) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rda" ,r-rda) + ("r-rpart" ,r-rpart) + ("r-sfsmisc" ,r-sfsmisc) + ("r-shiny" ,r-shiny) + ("r-threejs" ,r-threejs))) + (home-page "https://bioconductor.org/packages/MLInterfaces/") + (synopsis "Interfaces to R machine learning procedures") + (description + "This package provides uniform interfaces to machine learning code for +data in R and Bioconductor containers.") + ;; Any version of the LGPL. + (license license:lgpl2.1+))) -- cgit v1.2.3 From a793e88c5ed84f78fded2051649c06e1ac9a3efc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:15 +0100 Subject: gnu: Add r-annaffy. * gnu/packages/bioconductor.scm (r-annaffy): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 26ebb0930b..4cc9887d33 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2923,3 +2923,39 @@ profiles (GO and KEGG) of gene and gene clusters.") data in R and Bioconductor containers.") ;; Any version of the LGPL. (license license:lgpl2.1+))) + +(define-public r-annaffy + (package + (name "r-annaffy") + (version "1.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annaffy" version)) + (sha256 + (base32 + "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-reference-to-non-free-data + (lambda _ + (substitute* "DESCRIPTION" + ((", KEGG.db") "")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-dbi" ,r-dbi) + ("r-go-db" ,r-go-db))) + (home-page "https://bioconductor.org/packages/annaffy/") + (synopsis "Annotation tools for Affymetrix biological metadata") + (description + "This package provides functions for handling data from Bioconductor +Affymetrix annotation data packages. It produces compact HTML and text +reports including experimental data and URL links to many online databases. +It allows searching of biological metadata using various criteria.") + ;; Any version of the LGPL according to the DESCRIPTION file. A copy of + ;; the LGPL 2.1 is included. + (license license:lgpl2.1+))) -- cgit v1.2.3 From 0ec0a5ecc973d4f33260e00fa5448cc54a7c3a20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:24 +0100 Subject: gnu: Add r-a4core. * gnu/packages/bioconductor.scm (r-a4core): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4cc9887d33..4dffe978e9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2959,3 +2959,26 @@ It allows searching of biological metadata using various criteria.") ;; Any version of the LGPL according to the DESCRIPTION file. A copy of ;; the LGPL 2.1 is included. (license license:lgpl2.1+))) + +(define-public r-a4core + (package + (name "r-a4core") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Core" version)) + (sha256 + (base32 + "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr")))) + (properties `((upstream-name . "a4Core"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-glmnet" ,r-glmnet))) + (home-page "https://bioconductor.org/packages/a4Core") + (synopsis "Automated Affymetrix array analysis core package") + (description + "This is the core package for the automated analysis of Affymetrix +arrays.") + (license license:gpl3))) -- cgit v1.2.3 From 9ae37581e095c03b62a6b4231c3c26cca0e8fad6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:32 +0100 Subject: gnu: Add r-a4classif. * gnu/packages/bioconductor.scm (r-a4classif): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4dffe978e9..db691bcd88 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2982,3 +2982,31 @@ It allows searching of biological metadata using various criteria.") "This is the core package for the automated analysis of Affymetrix arrays.") (license license:gpl3))) + +(define-public r-a4classif + (package + (name "r-a4classif") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Classif" version)) + (sha256 + (base32 + "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j")))) + (properties `((upstream-name . "a4Classif"))) + (build-system r-build-system) + (propagated-inputs + `(("r-a4core" ,r-a4core) + ("r-a4preproc" ,r-a4preproc) + ("r-glmnet" ,r-glmnet) + ("r-mlinterfaces" ,r-mlinterfaces) + ("r-pamr" ,r-pamr) + ("r-rocr" ,r-rocr) + ("r-varselrf" ,r-varselrf))) + (home-page "https://bioconductor.org/packages/a4Classif/") + (synopsis "Automated Affymetrix array analysis classification package") + (description + "This is the classification package for the automated analysis of +Affymetrix arrays.") + (license license:gpl3))) -- cgit v1.2.3 From b8d13e2c0ee082b16f43930385cc34ce09ae4ef3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:41 +0100 Subject: gnu: Add r-a4preproc. * gnu/packages/bioconductor.scm (r-a4preproc): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db691bcd88..f7191d2d4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3010,3 +3010,25 @@ arrays.") "This is the classification package for the automated analysis of Affymetrix arrays.") (license license:gpl3))) + +(define-public r-a4preproc + (package + (name "r-a4preproc") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Preproc" version)) + (sha256 + (base32 + "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp")))) + (properties `((upstream-name . "a4Preproc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/a4Preproc/") + (synopsis "Automated Affymetrix array analysis preprocessing package") + (description + "This is a package for the automated analysis of Affymetrix arrays. It +is used for preprocessing the arrays.") + (license license:gpl3))) -- cgit v1.2.3 From 8e15f861399333ac8346458eba34ab3d94c69a27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:50 +0100 Subject: gnu: Add r-a4reporting. * gnu/packages/bioconductor.scm (r-a4reporting): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f7191d2d4e..bdf8938488 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3032,3 +3032,26 @@ Affymetrix arrays.") "This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.") (license license:gpl3))) + +(define-public r-a4reporting + (package + (name "r-a4reporting") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Reporting" version)) + (sha256 + (base32 + "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4")))) + (properties `((upstream-name . "a4Reporting"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annaffy" ,r-annaffy) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/a4Reporting/") + (synopsis "Automated Affymetrix array analysis reporting package") + (description + "This is a package for the automated analysis of Affymetrix arrays. It +provides reporting features.") + (license license:gpl3))) -- cgit v1.2.3 From dbfe33758627782302ff7c9bfa11640fb0900476 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:22:57 +0100 Subject: gnu: Add r-a4base. * gnu/packages/bioconductor.scm (r-a4base): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bdf8938488..7b849a0718 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3055,3 +3055,35 @@ is used for preprocessing the arrays.") "This is a package for the automated analysis of Affymetrix arrays. It provides reporting features.") (license license:gpl3))) + +(define-public r-a4base + (package + (name "r-a4base") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4Base" version)) + (sha256 + (base32 + "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70")))) + (properties `((upstream-name . "a4Base"))) + (build-system r-build-system) + (propagated-inputs + `(("r-a4core" ,r-a4core) + ("r-a4preproc" ,r-a4preproc) + ("r-annaffy" ,r-annaffy) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-genefilter" ,r-genefilter) + ("r-glmnet" ,r-glmnet) + ("r-gplots" ,r-gplots) + ("r-limma" ,r-limma) + ("r-mpm" ,r-mpm) + ("r-multtest" ,r-multtest))) + (home-page "https://bioconductor.org/packages/a4Base/") + (synopsis "Automated Affymetrix array analysis base package") + (description + "This package provides basic features for the automated analysis of +Affymetrix arrays.") + (license license:gpl3))) -- cgit v1.2.3 From 84ad024e2d0dff61aa6e1333886f314c72e250ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 28 Mar 2019 18:23:02 +0100 Subject: gnu: Add r-a4. * gnu/packages/bioconductor.scm (r-a4): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b849a0718..7facbc1957 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3087,3 +3087,28 @@ provides reporting features.") "This package provides basic features for the automated analysis of Affymetrix arrays.") (license license:gpl3))) + +(define-public r-a4 + (package + (name "r-a4") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "a4" version)) + (sha256 + (base32 + "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-a4base" ,r-a4base) + ("r-a4classif" ,r-a4classif) + ("r-a4core" ,r-a4core) + ("r-a4preproc" ,r-a4preproc) + ("r-a4reporting" ,r-a4reporting))) + (home-page "https://bioconductor.org/packages/a4/") + (synopsis "Automated Affymetrix array analysis umbrella package") + (description + "This package provides a software suite for the automated analysis of +Affymetrix arrays.") + (license license:gpl3))) -- cgit v1.2.3 From 59d331f16a9bdc8c2cbc42534ca0871907c21319 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 06:35:57 +0100 Subject: gnu: Add r-abseqr. * gnu/packages/bioconductor.scm (r-abseqr): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7facbc1957..2bb0e8509c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -29,6 +29,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) + #:use-module (gnu packages haskell) #:use-module (gnu packages maths) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) @@ -3112,3 +3113,49 @@ Affymetrix arrays.") "This package provides a software suite for the automated analysis of Affymetrix arrays.") (license license:gpl3))) + +(define-public r-abseqr + (package + (name "r-abseqr") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "abseqR" version)) + (sha256 + (base32 + "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry")))) + (properties `((upstream-name . "abseqR"))) + (build-system r-build-system) + (inputs + `(("pandoc" ,ghc-pandoc))) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-biocstyle" ,r-biocstyle) + ("r-circlize" ,r-circlize) + ("r-flexdashboard" ,r-flexdashboard) + ("r-ggcorrplot" ,r-ggcorrplot) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-knitr" ,r-knitr) + ("r-plotly" ,r-plotly) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-rmarkdown" ,r-rmarkdown) + ("r-stringr" ,r-stringr) + ("r-vegan" ,r-vegan) + ("r-venndiagram" ,r-venndiagram))) + (home-page "https://github.com/malhamdoosh/abseqR") + (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") + (description + "AbSeq is a comprehensive bioinformatic pipeline for the analysis of +sequencing datasets generated from antibody libraries and abseqR is one of its +packages. AbseqR empowers the users of abseqPy with plotting and reporting +capabilities and allows them to generate interactive HTML reports for the +convenience of viewing and sharing with other researchers. Additionally, +abseqR extends abseqPy to compare multiple repertoire analyses and perform +further downstream analysis on its output.") + (license license:gpl3))) -- cgit v1.2.3 From 41aab7d186d36876c3ad8202e4d78313235998d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 14:57:23 +0100 Subject: gnu: Add r-bacon. * gnu/packages/bioconductor.scm (r-bacon): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2bb0e8509c..48c6009864 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3159,3 +3159,28 @@ convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.") (license license:gpl3))) + +(define-public r-bacon + (package + (name "r-bacon") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bacon" version)) + (sha256 + (base32 + "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://bioconductor.org/packages/bacon/") + (synopsis "Controlling bias and inflation in association studies") + (description + "Bacon can be used to remove inflation and bias often observed in +epigenome- and transcriptome-wide association studies. To this end bacon +constructs an empirical null distribution using a Gibbs Sampling algorithm by +fitting a three-component normal mixture on z-scores.") + (license license:gpl2+))) -- cgit v1.2.3 From 051e8e1a5bec01952012cf7f1903cd72add0e25c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 14:59:12 +0100 Subject: gnu: Add r-rgadem. * gnu/packages/bioconductor.scm (r-rgadem): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 48c6009864..6df46ef379 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3184,3 +3184,28 @@ epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.") (license license:gpl2+))) + +(define-public r-rgadem + (package + (name "r-rgadem") + (version "2.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rGADEM" version)) + (sha256 + (base32 + "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2")))) + (properties `((upstream-name . "rGADEM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-iranges" ,r-iranges) + ("r-seqlogo" ,r-seqlogo))) + (home-page "https://bioconductor.org/packages/rGADEM/") + (synopsis "De novo sequence motif discovery") + (description + "rGADEM is an efficient de novo motif discovery tool for large-scale +genomic sequence data.") + (license license:artistic2.0))) -- cgit v1.2.3 From 229f97c37aef0f50d144524275315fd36cd5973a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 14:59:23 +0100 Subject: gnu: Add r-motiv. * gnu/packages/bioconductor.scm (r-motiv): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6df46ef379..63a1c9923c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3209,3 +3209,34 @@ fitting a three-component normal mixture on z-scores.") "rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.") (license license:artistic2.0))) + +(define-public r-motiv + (package + (name "r-motiv") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MotIV" version)) + (sha256 + (base32 + "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8")))) + (properties `((upstream-name . "MotIV"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-rgadem" ,r-rgadem) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/MotIV/") + (synopsis "Motif identification and validation") + (description + "This package is used for the identification and validation of sequence +motifs. It makes use of STAMP for comparing a set of motifs to a given +database (e.g. JASPAR). It can also be used to visualize motifs, motif +distributions, modules and filter motifs.") + (license license:gpl2))) -- cgit v1.2.3 From 2a72ef561b53b69210df2c1562f9d8ced35adabd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 15:39:55 +0100 Subject: gnu: Add r-motifstack. * gnu/packages/bioconductor.scm (r-motifstack): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63a1c9923c..af2d7ce335 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3240,3 +3240,34 @@ motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.") (license license:gpl2))) + +(define-public r-motifstack + (package + (name "r-motifstack") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifStack" version)) + (sha256 + (base32 + "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf")))) + (properties `((upstream-name . "motifStack"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-biostrings" ,r-biostrings) + ("r-grimport" ,r-grimport) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-motiv" ,r-motiv) + ("r-scales" ,r-scales) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/motifStack/") + (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") + (description + "The motifStack package is designed for graphic representation of +multiple motifs with different similarity scores. It works with both DNA/RNA +sequence motifs and amino acid sequence motifs. In addition, it provides the +flexibility for users to customize the graphic parameters such as the font +type and symbol colors.") + (license license:gpl2+))) -- cgit v1.2.3 From e5bff3079d673d1d7816b0c30142935ef1e05791 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 15:40:06 +0100 Subject: gnu: Add r-genomicscores. * gnu/packages/bioconductor.scm (r-genomicscores): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index af2d7ce335..0daea685e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3271,3 +3271,34 @@ sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.") (license license:gpl2+))) + +(define-public r-genomicscores + (package + (name "r-genomicscores") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicScores" version)) + (sha256 + (base32 + "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n")))) + (properties `((upstream-name . "GenomicScores"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml))) + (home-page "https://github.com/rcastelo/GenomicScores/") + (synopsis "Work with genome-wide position-specific scores") + (description + "This package provides infrastructure to store and access genome-wide +position-specific scores within R and Bioconductor.") + (license license:artistic2.0))) -- cgit v1.2.3 From 32e0f906d775679d8b4e770d267d29cb77724360 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 15:40:22 +0100 Subject: gnu: Add r-atacseqqc. * gnu/packages/bioconductor.scm (r-atacseqqc): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0daea685e5..4ee14a4c08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3302,3 +3302,47 @@ type and symbol colors.") "This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.") (license license:artistic2.0))) + +(define-public r-atacseqqc + (package + (name "r-atacseqqc") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ATACseqQC" version)) + (sha256 + (base32 + "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn")))) + (properties `((upstream-name . "ATACseqQC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-chippeakanno" ,r-chippeakanno) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicscores" ,r-genomicscores) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-motifstack" ,r-motifstack) + ("r-preseqr" ,r-preseqr) + ("r-randomforest" ,r-randomforest) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ATACseqQC/") + (synopsis "ATAC-seq quality control") + (description + "ATAC-seq, an assay for Transposase-Accessible Chromatin using +sequencing, is a rapid and sensitive method for chromatin accessibility +analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq +and DNAse-seq. The ATACseqQC package was developed to help users to quickly +assess whether their ATAC-seq experiment is successful. It includes +diagnostic plots of fragment size distribution, proportion of mitochondria +reads, nucleosome positioning pattern, and CTCF or other Transcript Factor +footprints.") + (license license:gpl2+))) -- cgit v1.2.3 From 692bce15953994e1c19c464a1d91f5222430a166 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 17:43:40 +0100 Subject: gnu: Add r-abadata. * gnu/packages/bioconductor.scm (r-abadata): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4ee14a4c08..c0f0520ce8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -738,6 +738,43 @@ Disease Ontology.") ;;; Experiment data +(define-public r-abadata + (package + (name "r-abadata") + (version "1.12.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ABAData_" version ".tar.gz")) + (sha256 + (base32 + "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) + (properties + `((upstream-name . "ABAData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://www.bioconductor.org/packages/ABAData/") + (synopsis "Gene expression in human brain regions from Allen Brain Atlas") + (description + "This package provides the data for the gene expression enrichment +analysis conducted in the package ABAEnrichment. The package includes three +datasets which are derived from the Allen Brain Atlas: + +@enumerate +@item Gene expression data from Human Brain (adults) averaged across donors, +@item Gene expression data from the Developing Human Brain pooled into five + age categories and averaged across donors, and +@item a developmental effect score based on the Developing Human Brain + expression data. +@end enumerate + +All datasets are restricted to protein coding genes.") + (license license:gpl2+))) + (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") -- cgit v1.2.3 From 3972cfce6a03c8714c2b762b8d573e833efd8aee Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 17:43:52 +0100 Subject: gnu: Add r-gofuncr. * gnu/packages/bioconductor.scm (r-gofuncr): New variable. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c0f0520ce8..fb7e5a95f3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3383,3 +3383,50 @@ diagnostic plots of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.") (license license:gpl2+))) + +(define-public r-gofuncr + (package + (name "r-gofuncr") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOfuncR" version)) + (sha256 + (base32 + "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk")))) + (properties `((upstream-name . "GOfuncR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-mapplots" ,r-mapplots) + ("r-rcpp" ,r-rcpp) + ("r-vioplot" ,r-vioplot))) + (home-page "https://bioconductor.org/packages/GOfuncR/") + (synopsis "Gene ontology enrichment using FUNC") + (description + "GOfuncR performs a gene ontology enrichment analysis based on the +ontology enrichment software FUNC. GO-annotations are obtained from +OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is +included in the package and updated regularly. GOfuncR provides the standard +candidate vs background enrichment analysis using the hypergeometric test, as +well as three additional tests: + +@enumerate +@item the Wilcoxon rank-sum test that is used when genes are ranked, +@item a binomial test that is used when genes are associated with two counts, + and +@item a Chi-square or Fisher's exact test that is used in cases when genes are +associated with four counts. +@end enumerate + +To correct for multiple testing and interdependency of the tests, family-wise +error rates are computed based on random permutations of the gene-associated +variables. GOfuncR also provides tools for exploring the ontology graph and +the annotations, and options to take gene-length or spatial clustering of +genes into account. It is also possible to provide custom gene coordinates, +annotations and ontologies.") + (license license:gpl2+))) -- cgit v1.2.3 From 9bf4bb19c9f4a85fb7ea96f9f70add9b2a1513db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 17:43:57 +0100 Subject: gnu: Add r-abaenrichment. * gnu/packages/bioconductor.scm (r-abaenrichment): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb7e5a95f3..cbde3b54b0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3430,3 +3430,33 @@ the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.") (license license:gpl2+))) + +(define-public r-abaenrichment + (package + (name "r-abaenrichment") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ABAEnrichment" version)) + (sha256 + (base32 + "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v")))) + (properties `((upstream-name . "ABAEnrichment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abadata" ,r-abadata) + ("r-data-table" ,r-data-table) + ("r-gofuncr" ,r-gofuncr) + ("r-gplots" ,r-gplots) + ("r-gtools" ,r-gtools) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/ABAEnrichment/") + (synopsis "Gene expression enrichment in human brain regions") + (description + "The package ABAEnrichment is designed to test for enrichment of user +defined candidate genes in the set of expressed genes in different human brain +regions. The core function @code{aba_enrich} integrates the expression of the +candidate gene set (averaged across donors) and the structural information of +the brain using an ontology, both provided by the Allen Brain Atlas project.") + (license license:gpl2+))) -- cgit v1.2.3 From 0b91b7b969567e2f149606ab76ec34d332a52db6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 17:49:54 +0100 Subject: gnu: Add r-annotationfuncs. * gnu/packages/bioconductor.scm (r-annotationfuncs): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cbde3b54b0..599f774042 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3460,3 +3460,28 @@ regions. The core function @code{aba_enrich} integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.") (license license:gpl2+))) + +(define-public r-annotationfuncs + (package + (name "r-annotationfuncs") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFuncs" version)) + (sha256 + (base32 + "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss")))) + (properties + `((upstream-name . "AnnotationFuncs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi))) + (home-page "https://www.iysik.com/r/annotationfuncs") + (synopsis "Annotation translation functions") + (description + "This package provides functions for handling translating between +different identifieres using the Biocore Data Team data-packages (e.g. +@code{org.Bt.eg.db}).") + (license license:gpl2))) -- cgit v1.2.3 From adf7d8135b6fbb96d9d263760e749a7ada21754b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 18:05:45 +0100 Subject: gnu: Add r-annotationtools. * gnu/packages/bioconductor.scm (r-annotationtools): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 599f774042..be618d39b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3485,3 +3485,28 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") different identifieres using the Biocore Data Team data-packages (e.g. @code{org.Bt.eg.db}).") (license license:gpl2))) + +(define-public r-annotationtools + (package + (name "r-annotationtools") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "annotationTools" version)) + (sha256 + (base32 + "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z")))) + (properties + `((upstream-name . "annotationTools"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/annotationTools/") + (synopsis "Annotate microarrays and perform gene expression analyses") + (description + "This package provides functions to annotate microarrays, find orthologs, +and integrate heterogeneous gene expression profiles using annotation and +other molecular biology information available as flat file database (plain +text files).") + ;; Any version of the GPL. + (license (list license:gpl2+)))) -- cgit v1.2.3 From f31e10f82e3bcfa74901f87b4a3d951758861804 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 18:07:17 +0100 Subject: gnu: Add r-allelicimbalance. * gnu/packages/bioconductor.scm (r-allelicimbalance): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be618d39b9..2d74d2628c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3510,3 +3510,44 @@ other molecular biology information available as flat file database (plain text files).") ;; Any version of the GPL. (license (list license:gpl2+)))) + +(define-public r-allelicimbalance + (package + (name "r-allelicimbalance") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AllelicImbalance" version)) + (sha256 + (base32 + "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91")))) + (properties + `((upstream-name . "AllelicImbalance"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-gridextra" ,r-gridextra) + ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-nlme" ,r-nlme) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/pappewaio/AllelicImbalance") + (synopsis "Investigate allele-specific expression") + (description + "This package provides a framework for allele-specific expression +investigation using RNA-seq data.") + (license license:gpl3))) -- cgit v1.2.3 From ffe7029babb40481f50cf931b28e92c8f74dfe01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 18:10:46 +0100 Subject: gnu: Add r-aucell. * gnu/packages/bioconductor.scm (r-aucell): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d74d2628c..6a7c98f625 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3551,3 +3551,38 @@ text files).") "This package provides a framework for allele-specific expression investigation using RNA-seq data.") (license license:gpl3))) + +(define-public r-aucell + (package + (name "r-aucell") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AUCell" version)) + (sha256 + (base32 + "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9")))) + (properties `((upstream-name . "AUCell"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-gseabase" ,r-gseabase) + ("r-mixtools" ,r-mixtools) + ("r-r-utils" ,r-r-utils) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/AUCell/") + (synopsis "Analysis of gene set activity in single-cell RNA-seq data") + (description + "AUCell allows to identify cells with active gene sets (e.g. signatures, +gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area +Under the Curve} (AUC) to calculate whether a critical subset of the input +gene set is enriched within the expressed genes for each cell. The +distribution of AUC scores across all the cells allows exploring the relative +expression of the signature. Since the scoring method is ranking-based, +AUCell is independent of the gene expression units and the normalization +procedure. In addition, since the cells are evaluated individually, it can +easily be applied to bigger datasets, subsetting the expression matrix if +needed.") + (license license:gpl3))) -- cgit v1.2.3 From 5cfa4bff697fa0af43f6a7bbde7ec23c8a146e10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 19:28:03 +0100 Subject: gnu: Add r-ebimage. * gnu/packages/bioconductor.scm (r-ebimage): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6a7c98f625..f6ffacc04e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -30,6 +30,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages haskell) + #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) @@ -3586,3 +3587,42 @@ procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.") (license license:gpl3))) + +(define-public r-ebimage + (package + (name "r-ebimage") + (version "4.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EBImage" version)) + (sha256 + (base32 + "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx")))) + (properties `((upstream-name . "EBImage"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-biocgenerics" ,r-biocgenerics) + ("r-fftwtools" ,r-fftwtools) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jpeg" ,r-jpeg) + ("r-locfit" ,r-locfit) + ("r-png" ,r-png) + ("r-rcurl" ,r-rcurl) + ("r-tiff" ,r-tiff))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/aoles/EBImage") + (synopsis "Image processing and analysis toolbox for R") + (description + "EBImage provides general purpose functionality for image processing and +analysis. In the context of (high-throughput) microscopy-based cellular +assays, EBImage offers tools to segment cells and extract quantitative +cellular descriptors. This allows the automation of such tasks using the R +programming language and facilitates the use of other tools in the R +environment for signal processing, statistical modeling, machine learning and +visualization with image data.") + ;; Any version of the LGPL. + (license license:lgpl2.1+))) -- cgit v1.2.3 From 51e98f7e0fb1dc6578e2ad7c972fb419b25bba16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 19:28:11 +0100 Subject: gnu: Add r-yamss. * gnu/packages/bioconductor.scm (r-yamss): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6ffacc04e..b0e5d06988 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3626,3 +3626,35 @@ environment for signal processing, statistical modeling, machine learning and visualization with image data.") ;; Any version of the LGPL. (license license:lgpl2.1+))) + +(define-public r-yamss + (package + (name "r-yamss") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yamss" version)) + (sha256 + (base32 + "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-ebimage" ,r-ebimage) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-mzr" ,r-mzr) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" + ,r-summarizedexperiment))) + (home-page "https://github.com/hansenlab/yamss") + (synopsis "Tools for high-throughput metabolomics") + (description + "This package provides tools to analyze and visualize high-throughput +metabolomics data aquired using chromatography-mass spectrometry. These tools +preprocess data in a way that enables reliable and powerful differential +analysis.") + (license license:artistic2.0))) -- cgit v1.2.3 From 398c4a93471067698efc965d4de03d66b2b9738e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 20:28:28 +0100 Subject: gnu: Add r-gtrellis. * gnu/packages/bioconductor.scm (r-gtrellis): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0e5d06988..d3ffd41a3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3658,3 +3658,30 @@ metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.") (license license:artistic2.0))) + +(define-public r-gtrellis + (package + (name "r-gtrellis") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gtrellis" version)) + (sha256 + (base32 + "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-genomicranges" ,r-genomicranges) + ("r-getoptlong" ,r-getoptlong) + ("r-iranges" ,r-iranges))) + (home-page "https://github.com/jokergoo/gtrellis") + (synopsis "Genome level Trellis layout") + (description + "Genome level Trellis graph visualizes genomic data conditioned by +genomic categories (e.g. chromosomes). For each genomic category, multiple +dimensional data which are represented as tracks describe different features +from different aspects. This package provides high flexibility to arrange +genomic categories and to add self-defined graphics in the plot.") + (license license:expat))) -- cgit v1.2.3 From 28098414d0e1455110b9ee8a500255f93dc34e20 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 20:28:38 +0100 Subject: gnu: Add r-somaticsignatures. * gnu/packages/bioconductor.scm (r-somaticsignatures): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d3ffd41a3c..78fd5a989b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3685,3 +3685,40 @@ dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.") (license license:expat))) + +(define-public r-somaticsignatures + (package + (name "r-somaticsignatures") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SomaticSignatures" version)) + (sha256 + (base32 + "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02")))) + (properties + `((upstream-name . "SomaticSignatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-nmf" ,r-nmf) + ("r-pcamethods" ,r-pcamethods) + ("r-proxy" ,r-proxy) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/juliangehring/SomaticSignatures") + (synopsis "Somatic signatures") + (description + "This package identifies mutational signatures of @dfn{single nucleotide +variants} (SNVs). It provides a infrastructure related to the methodology +described in Nik-Zainal (2012, Cell), with flexibility in the matrix +decomposition algorithms.") + (license license:expat))) -- cgit v1.2.3 From 303f2ed1c6447bd01e5310ea16aec6cbd0153a5b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 20:28:46 +0100 Subject: gnu: Add r-yapsa. * gnu/packages/bioconductor.scm (r-yapsa): New variable. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 78fd5a989b..4c31ffcc0d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3722,3 +3722,43 @@ variants} (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.") (license license:expat))) + +(define-public r-yapsa + (package + (name "r-yapsa") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "YAPSA" version)) + (sha256 + (base32 + "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j")))) + (properties `((upstream-name . "YAPSA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-circlize" ,r-circlize) + ("r-complexheatmap" ,r-complexheatmap) + ("r-corrplot" ,r-corrplot) + ("r-dendextend" ,r-dendextend) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-getoptlong" ,r-getoptlong) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtrellis" ,r-gtrellis) + ("r-keggrest" ,r-keggrest) + ("r-lsei" ,r-lsei) + ("r-pmcmr" ,r-pmcmr) + ("r-reshape2" ,r-reshape2) + ("r-somaticsignatures" ,r-somaticsignatures) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/YAPSA/") + (synopsis "Yet another package for signature analysis") + (description + "This package provides functions and routines useful in the analysis of +somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, +functions to perform a signature analysis with known signatures and a +signature analysis on @dfn{stratified mutational catalogue} (SMC) are +provided.") + (license license:gpl3))) -- cgit v1.2.3 From e99380d67b459128807f27184b93f0b2a9e6c3fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:18:49 +0100 Subject: gnu: Add r-gcrma. * gnu/packages/bioconductor.scm (r-gcrma): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4c31ffcc0d..91a5a66ec2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3762,3 +3762,39 @@ functions to perform a signature analysis with known signatures and a signature analysis on @dfn{stratified mutational catalogue} (SMC) are provided.") (license license:gpl3))) + +(define-public r-gcrma + (package + (name "r-gcrma") + (version "2.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gcrma" version)) + (sha256 + (base32 + "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-biostrings" ,r-biostrings) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/gcrma/") + (synopsis "Background adjustment using sequence information") + (description + "Gcrma adjusts for background intensities in Affymetrix array data which +include optical noise and @dfn{non-specific binding} (NSB). The main function +@code{gcrma} converts background adjusted probe intensities to expression +measures using the same normalization and summarization methods as a +@dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information +to estimate probe affinity to NSB. The sequence information is summarized in +a more complex way than the simple GC content. Instead, the base types (A, T, +G or C) at each position along the probe determine the affinity of each probe. +The parameters of the position-specific base contributions to the probe +affinity is estimated in an NSB experiment in which only NSB but no +gene-specific bidning is expected.") + ;; Any version of the LGPL + (license license:lgpl2.1+))) -- cgit v1.2.3 From 4675b3cfa3dbf13056dec550d5a72fbf4a73def7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:19:30 +0100 Subject: gnu: Add r-simpleaffy. * gnu/packages/bioconductor.scm (r-simpleaffy): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91a5a66ec2..ade51157c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3798,3 +3798,31 @@ affinity is estimated in an NSB experiment in which only NSB but no gene-specific bidning is expected.") ;; Any version of the LGPL (license license:lgpl2.1+))) + +(define-public r-simpleaffy + (package + (name "r-simpleaffy") + (version "2.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "simpleaffy" version)) + (sha256 + (base32 + "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-gcrma" ,r-gcrma) + ("r-genefilter" ,r-genefilter))) + (home-page "https://bioconductor.org/packages/simpleaffy/") + (synopsis "Very simple high level analysis of Affymetrix data") + (description + "This package provides high level functions for reading Affy @file{.CEL} +files, phenotypic data, and then computing simple things with it, such as +t-tests, fold changes and the like. It makes heavy use of the @code{affy} +library. It also has some basic scatter plot functions and mechanisms for +generating high resolution journal figures.") + (license license:gpl2+))) -- cgit v1.2.3 From f562c90aa8883e1edf4f2e977522293640949d68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:19:42 +0100 Subject: gnu: Add r-yaqcaffy. * gnu/packages/bioconductor.scm (r-yaqcaffy): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ade51157c4..42779d264c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3826,3 +3826,25 @@ t-tests, fold changes and the like. It makes heavy use of the @code{affy} library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.") (license license:gpl2+))) + +(define-public r-yaqcaffy + (package + (name "r-yaqcaffy") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yaqcaffy" version)) + (sha256 + (base32 + "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-simpleaffy" ,r-simpleaffy))) + (home-page "https://bioconductor.org/packages/yaqcaffy/") + (synopsis "Affymetrix quality control and reproducibility analysis") + (description + "This is a package that can be used for quality control of Affymetrix +GeneChip expression data and reproducibility analysis of human whole genome +chips with the MAQC reference datasets.") + (license license:artistic2.0))) -- cgit v1.2.3 From 59cf26292f8aa13c4a98687371a2dafa63ccc932 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:30:39 +0100 Subject: gnu: Add r-quantro. * gnu/packages/bioconductor.scm (r-quantro): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42779d264c..6b11b47eae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3848,3 +3848,34 @@ generating high resolution journal figures.") GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.") (license license:artistic2.0))) + +(define-public r-quantro + (package + (name "r-quantro") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "quantro" version)) + (sha256 + (base32 + "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-minfi" ,r-minfi) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/quantro/") + (synopsis "Test for when to use quantile normalization") + (description + "This package provides a data-driven test for the assumptions of quantile +normalization using raw data such as objects that inherit eSets (e.g. +ExpressionSet, MethylSet). Group level information about each sample (such as +Tumor / Normal status) must also be provided because the test assesses if +there are global differences in the distributions between the user-defined +groups.") + (license license:gpl3+))) -- cgit v1.2.3 From 98a2af31a8066eff780a71a6366749cad5d3d580 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:30:47 +0100 Subject: gnu: Add r-yarn. * gnu/packages/bioconductor.scm (r-yarn): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6b11b47eae..b0c1fb08bf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3879,3 +3879,38 @@ Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.") (license license:gpl3+))) + +(define-public r-yarn + (package + (name "r-yarn") + (version "1.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "yarn" version)) + (sha256 + (base32 + "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biomart" ,r-biomart) + ("r-downloader" ,r-downloader) + ("r-edger" ,r-edger) + ("r-gplots" ,r-gplots) + ("r-limma" ,r-limma) + ("r-matrixstats" ,r-matrixstats) + ("r-preprocesscore" ,r-preprocesscore) + ("r-quantro" ,r-quantro) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-readr" ,r-readr))) + (home-page "https://bioconductor.org/packages/yarn/") + (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") + (description + "Expedite large RNA-Seq analyses using a combination of previously +developed tools. YARN is meant to make it easier for the user in performing +basic mis-annotation quality control, filtering, and condition-aware +normalization. YARN leverages many Bioconductor tools and statistical +techniques to account for the large heterogeneity and sparsity found in very +large RNA-seq experiments.") + (license license:artistic2.0))) -- cgit v1.2.3 From a6e1eb1a96799212815eda7b0408d778b7000022 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:41:58 +0100 Subject: gnu: Add r-roar. * gnu/packages/bioconductor.scm (r-roar): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b0c1fb08bf..d87d9135ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3914,3 +3914,32 @@ normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.") (license license:artistic2.0))) + +(define-public r-roar + (package + (name "r-roar") + (version "1.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "roar" version)) + (sha256 + (base32 + "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://github.com/vodkatad/roar/") + (synopsis "Identify differential APA usage from RNA-seq alignments") + (description + "This package provides tools for identifying preferential usage of APA +sites, comparing two biological conditions, starting from known alternative +sites and alignments obtained from standard RNA-seq experiments.") + (license license:gpl3))) -- cgit v1.2.3 From 50d91770513bb52bd693080661758d8fd6aab89f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:42:19 +0100 Subject: gnu: Add r-xbseq. * gnu/packages/bioconductor.scm (r-xbseq): New variable. --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d87d9135ff..c276f000b6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3943,3 +3943,40 @@ large RNA-seq experiments.") sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.") (license license:gpl3))) + +(define-public r-xbseq + (package + (name "r-xbseq") + (version "1.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XBSeq" version)) + (sha256 + (base32 + "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph")))) + (properties `((upstream-name . "XBSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-locfit" ,r-locfit) + ("r-magrittr" ,r-magrittr) + ("r-matrixstats" ,r-matrixstats) + ("r-pracma" ,r-pracma) + ("r-roar" ,r-roar))) + (home-page "https://github.com/Liuy12/XBSeq") + (synopsis "Test for differential expression for RNA-seq data") + (description + "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential +expression} (DE), where a statistical model was established based on the +assumption that observed signals are the convolution of true expression +signals and sequencing noises. The mapped reads in non-exonic regions are +considered as sequencing noises, which follows a Poisson distribution. Given +measurable observed signal and background noise from RNA-seq data, true +expression signals, assuming governed by the negative binomial distribution, +can be delineated and thus the accurate detection of differential expressed +genes.") + (license license:gpl3+))) -- cgit v1.2.3 From c8310056f45e7395976773ada517aee1d41c2d9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:55:56 +0100 Subject: gnu: Add r-massspecwavelet. * gnu/packages/bioconductor.scm (r-massspecwavelet): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c276f000b6..4a73edf02c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3980,3 +3980,27 @@ expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.") (license license:gpl3+))) + +(define-public r-massspecwavelet + (package + (name "r-massspecwavelet") + (version "1.48.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MassSpecWavelet" version)) + (sha256 + (base32 + "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz")))) + (properties + `((upstream-name . "MassSpecWavelet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-waveslim" ,r-waveslim))) + (home-page "https://bioconductor.org/packages/MassSpecWavelet/") + (synopsis "Mass spectrum processing by wavelet-based algorithms") + (description + "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) +data mainly through the use of wavelet transforms. It supports peak detection +based on @dfn{Continuous Wavelet Transform} (CWT).") + (license license:lgpl2.0+))) -- cgit v1.2.3 From ec12e53736f212d700587e096ebee15ffc118c46 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Mar 2019 22:56:12 +0100 Subject: gnu: Add r-xcms. * gnu/packages/bioconductor.scm (r-xcms): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4a73edf02c..750311fd7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4004,3 +4004,39 @@ genes.") data mainly through the use of wavelet transforms. It supports peak detection based on @dfn{Continuous Wavelet Transform} (CWT).") (license license:lgpl2.0+))) + +(define-public r-xcms + (package + (name "r-xcms") + (version "3.4.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xcms" version)) + (sha256 + (base32 + "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-lattice" ,r-lattice) + ("r-massspecwavelet" ,r-massspecwavelet) + ("r-msnbase" ,r-msnbase) + ("r-multtest" ,r-multtest) + ("r-mzr" ,r-mzr) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-rann" ,r-rann) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-robustbase" ,r-robustbase) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/xcms/") + (synopsis "LC/MS and GC/MS mass spectrometry data analysis") + (description + "This package provides a framework for processing and visualization of +chromatographically separated and single-spectra mass spectral data. It +imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses +data for high-throughput, untargeted analyte profiling.") + (license license:gpl2+))) -- cgit v1.2.3 From 8830664d614f6a84df6f5153eee85761a20d24ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:12:06 +0200 Subject: gnu: Add r-wrench. * gnu/packages/bioconductor.scm (r-wrench): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 750311fd7b..b09d1957d8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4040,3 +4040,27 @@ chromatographically separated and single-spectra mass spectral data. It imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.") (license license:gpl2+))) + +(define-public r-wrench + (package + (name "r-wrench") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Wrench" version)) + (sha256 + (base32 + "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg")))) + (properties `((upstream-name . "Wrench"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats))) + (home-page "https://github.com/HCBravoLab/Wrench") + (synopsis "Wrench normalization for sparse count data") + (description + "Wrench is a package for normalization sparse genomic count data, like +that arising from 16s metagenomic surveys.") + (license license:artistic2.0))) -- cgit v1.2.3 From b9b8b447ec63df1bec74d60bc5f0020b0d79bd28 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:13:05 +0200 Subject: gnu: Add r-wiggleplotr. * gnu/packages/bioconductor.scm (r-wiggleplotr): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b09d1957d8..02688ce473 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4064,3 +4064,35 @@ data for high-throughput, untargeted analyte profiling.") "Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.") (license license:artistic2.0))) + +(define-public r-wiggleplotr + (package + (name "r-wiggleplotr") + (version "1.6.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wiggleplotr" version)) + (sha256 + (base32 + "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-purrr" ,r-purrr) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/wiggleplotr/") + (synopsis "Make read coverage plots from BigWig files") + (description + "This package provides tools to visualize read coverage from sequencing +experiments together with genomic annotations (genes, transcripts, peaks). +Introns of long transcripts can be rescaled to a fixed length for better +visualization of exonic read coverage.") + (license license:asl2.0))) -- cgit v1.2.3 From 7b5101c5bf9fb33768ae90e0e32ba2f67a491bc3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:16:02 +0200 Subject: gnu: Add r-widgettools. * gnu/packages/bioconductor.scm (r-widgettools): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 02688ce473..61ea05a7a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4096,3 +4096,24 @@ experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of exonic read coverage.") (license license:asl2.0))) + +(define-public r-widgettools + (package + (name "r-widgettools") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "widgetTools" version)) + (sha256 + (base32 + "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf")))) + (properties `((upstream-name . "widgetTools"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/widgetTools/") + (synopsis "Tools for creating interactive tcltk widgets") + (description + "This packages contains tools to support the construction of tcltk +widgets in R.") + ;; Any version of the LGPL. + (license license:lgpl3+))) -- cgit v1.2.3 From 6b12f213633e035e8b6eb61c36cfdbd19b434754 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:24:54 +0200 Subject: gnu: Add r-webbioc. * gnu/packages/bioconductor.scm (r-webbioc): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61ea05a7a7..7928a10679 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -32,6 +32,8 @@ #:use-module (gnu packages haskell) #:use-module (gnu packages image) #:use-module (gnu packages maths) + #:use-module (gnu packages netpbm) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web)) @@ -4117,3 +4119,36 @@ visualization of exonic read coverage.") widgets in R.") ;; Any version of the LGPL. (license license:lgpl3+))) + +(define-public r-webbioc + (package + (name "r-webbioc") + (version "1.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "webbioc" version)) + (sha256 + (base32 + "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi")))) + (build-system r-build-system) + (inputs + `(("netpbm" ,netpbm) + ("perl" ,perl))) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-annaffy" ,r-annaffy) + ("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-gcrma" ,r-gcrma) + ("r-multtest" ,r-multtest) + ("r-qvalue" ,r-qvalue) + ("r-vsn" ,r-vsn))) + (home-page "https://www.bioconductor.org/") + (synopsis "Bioconductor web interface") + (description + "This package provides an integrated web interface for doing microarray +analysis using several of the Bioconductor packages. It is intended to be +deployed as a centralized bioinformatics resource for use by many users. +Currently only Affymetrix oligonucleotide analysis is supported.") + (license license:gpl2+))) -- cgit v1.2.3 From 9800d859a74faba183f6d6e3d2957f4e0c5002e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:29:49 +0200 Subject: gnu: Add r-zfpkm. * gnu/packages/bioconductor.scm (r-zfpkm): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7928a10679..3800c2472e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4152,3 +4152,30 @@ analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) + +(define-public r-zfpkm + (package + (name "r-zfpkm") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zFPKM" version)) + (sha256 + (base32 + "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5")))) + (properties `((upstream-name . "zFPKM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-checkmate" ,r-checkmate) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/ronammar/zFPKM/") + (synopsis "Functions to facilitate zFPKM transformations") + (description + "This is a package to perform the zFPKM transform on RNA-seq FPKM data. +This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID +24215113).") + (license license:gpl3))) -- cgit v1.2.3 From 2bdc88fce75495496f1d7af65f1cadd1e5f51a66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 16:59:36 +0200 Subject: gnu: Add r-rbowtie2. * gnu/packages/bioconductor.scm (r-rbowtie2): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3800c2472e..823282397c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4179,3 +4179,26 @@ Currently only Affymetrix oligonucleotide analysis is supported.") This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).") (license license:gpl3))) + +(define-public r-rbowtie2 + (package + (name "r-rbowtie2") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rbowtie2" version)) + (sha256 + (base32 + "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr")))) + (properties `((upstream-name . "Rbowtie2"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/Rbowtie2/") + (synopsis "R wrapper for Bowtie2 and AdapterRemoval") + (description + "This package provides an R wrapper of the popular @code{bowtie2} +sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for +rapid adapter trimming, identification, and read merging.") + (license license:gpl3+))) -- cgit v1.2.3 From 5622628fd1a6e849b9ccebc37a944d892acb4c51 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 17:07:08 +0200 Subject: gnu: Add r-progeny. * gnu/packages/bioconductor.scm (r-progeny): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 823282397c..d033258d17 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4202,3 +4202,25 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for rapid adapter trimming, identification, and read merging.") (license license:gpl3+))) + +(define-public r-progeny + (package + (name "r-progeny") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "progeny" version)) + (sha256 + (base32 + "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7")))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://github.com/saezlab/progeny") + (synopsis "Pathway responsive gene activity inference") + (description + "This package provides a function to infer pathway activity from gene +expression. It contains the linear model inferred in the publication +\"Perturbation-response genes reveal signaling footprints in cancer gene +expression\".") + (license license:asl2.0))) -- cgit v1.2.3 From b50c966087b908e046da06e330c01e6d7a1ae9ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 17:41:54 +0200 Subject: gnu: Add r-arrmdata. * gnu/packages/bioconductor.scm (r-arrmdata): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d033258d17..b949b894c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -778,6 +778,30 @@ datasets which are derived from the Allen Brain Atlas: All datasets are restricted to protein coding genes.") (license license:gpl2+))) +(define-public r-arrmdata + (package + (name "r-arrmdata") + (version "1.18.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ARRmData_" version ".tar.gz")) + (sha256 + (base32 + "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) + (properties + `((upstream-name . "ARRmData"))) + (build-system r-build-system) + (home-page "https://www.bioconductor.org/packages/ARRmData/") + (synopsis "Example dataset for normalization of Illumina 450k methylation data") + (description + "This package provides raw beta values from 36 samples across 3 groups +from Illumina 450k methylation arrays.") + (license license:artistic2.0))) + (define-public r-hsmmsinglecell (package (name "r-hsmmsinglecell") -- cgit v1.2.3 From 307586c1e3b3fce8a9acc6f494f4972e6d4c3a79 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Apr 2019 17:42:01 +0200 Subject: gnu: Add r-arrmnormalization. * gnu/packages/bioconductor.scm (r-arrmnormalization): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b949b894c5..3eabedf076 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4248,3 +4248,26 @@ expression. It contains the linear model inferred in the publication \"Perturbation-response genes reveal signaling footprints in cancer gene expression\".") (license license:asl2.0))) + +(define-public r-arrmnormalization + (package + (name "r-arrmnormalization") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ARRmNormalization" version)) + (sha256 + (base32 + "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd")))) + (properties + `((upstream-name . "ARRmNormalization"))) + (build-system r-build-system) + (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (home-page "https://bioconductor.org/packages/ARRmNormalization/") + (synopsis "Adaptive robust regression normalization for methylation data") + (description + "This is a package to perform the @dfn{Adaptive Robust Regression +method} (ARRm) for the normalization of methylation data from the Illumina +Infinium HumanMethylation 450k assay.") + (license license:artistic2.0))) -- cgit v1.2.3 From bb94f7257e94b3180f1a65e232ed0d418c4a7984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 6 Apr 2019 23:01:59 +0200 Subject: gnu: r-inspect: Update to 1.12.2. * gnu/packages/bioconductor.scm (r-inspect): Update to 1.12.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3eabedf076..34650e149d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1621,14 +1621,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) + "1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2da8588ebcb85f70f5e3c9c3a7b4755a4d9bbd96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 6 Apr 2019 23:02:12 +0200 Subject: gnu: r-mlinterfaces: Update to 1.62.1. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.62.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 34650e149d..a77114f723 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2951,14 +2951,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.62.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8")))) + "1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9b19734c50a2f377e474e37cde15291b3fdf524a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 24 Apr 2019 19:40:51 +0200 Subject: gnu: r-yamss: Fix typo in description. * gnu/packages/bioconductor.scm (r-yamss)[description]: Fix typo. --- gnu/packages/bioconductor.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a77114f723..deb179c4d9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3680,7 +3680,7 @@ visualization with image data.") (synopsis "Tools for high-throughput metabolomics") (description "This package provides tools to analyze and visualize high-throughput -metabolomics data aquired using chromatography-mass spectrometry. These tools +metabolomics data acquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.") (license license:artistic2.0))) -- cgit v1.2.3