diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 149 |
1 files changed, 149 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a25f56ad02..44bf5c7d24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1518,6 +1518,36 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-dearseq + (package + (name "r-dearseq") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dearseq" version)) + (sha256 + (base32 + "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-kernsmooth" ,r-kernsmooth) + ("r-matrixstats" ,r-matrixstats) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-statmod" ,r-statmod) + ("r-survey" ,r-survey) + ("r-viridislite" ,r-kernsmooth))) + (home-page "https://github.com/borishejblum/dearseq") + (synopsis "DEA for RNA-seq data through a robust variance component test") + (description + "This is a package for Differential Expression Analysis of RNA-seq data. +It features a variance component score test accounting for data +heteroscedasticity through precision weights. Perform both gene-wise and gene +set analyses, and can deal with repeated or longitudinal data.") + (license license:gpl2))) + (define-public r-decipher (package (name "r-decipher") @@ -1638,6 +1668,41 @@ spent loading the full derfinder package when running the F-statistics calculation in parallel.") (license license:artistic2.0))) +(define-public r-drimseq + (package + (name "r-drimseq") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DRIMSeq" version)) + (sha256 + (base32 "0y2jb0hb633id038zmwnfny6h4ai77fdyy02f77vha1z8xg5nl02")))) + (properties `((upstream-name . "DRIMSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-edger" ,r-edger) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DRIMSeq") + (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") + (description + "The package provides two frameworks. One for the differential +transcript usage analysis between different conditions and one for the tuQTL +analysis. Both are based on modeling the counts of genomic features (i.e., +transcripts) with the Dirichlet-multinomial distribution. The package also +makes available functions for visualization and exploration of the data and +results.") + (license license:gpl3+))) + (define-public r-bluster (package (name "r-bluster") @@ -1721,6 +1786,59 @@ naming and share the same rich and consistent \"Vector API\" as much as possible.") (license license:artistic2.0))) +(define-public r-isoformswitchanalyzer + (package + (name "r-isoformswitchanalyzer") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) + (sha256 + (base32 "14bqf39gw5ab5r9sr3afkig1jbzdvds1bmcvc6bpb45kschx7fwf")))) + (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dbi" ,r-dbi) + ("r-dexseq" ,r-dexseq) + ("r-dplyr" ,r-dplyr) + ("r-drimseq" ,r-drimseq) + ("r-edger" ,r-edger) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-plyr" ,r-plyr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcurl" ,r-rcurl) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rtracklayer" ,r-rtracklayer) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tximeta" ,r-tximeta) + ("r-tximport" ,r-tximport) + ("r-venndiagram" ,r-venndiagram) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/") + (synopsis "Analyze alternative splicing in RNA-seq data") + (description + "This is a package for the analysis of alternative splicing and isoform +switches with predicted functional consequences (e.g. gain/loss of protein +domains etc.) from quantification of all types of RNASeq by tools such as +Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") + (license license:gpl2+))) + ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package @@ -6734,6 +6852,37 @@ required source code files from the official Leidenalg distribution and several functions from the R igraph package.") (license license:gpl3+)))) +(define-public r-sanssouci + ;; sansscouci doesn't have a (versioned) release yet. + ;; This is the latest commit as of packaging for Guix. + (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f") + (revision "1")) + (package + (name "r-sanssouci") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pneuvial/sanssouci.git") + (commit commit))) + (sha256 + (base32 + "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-generics" ,r-generics) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://pneuvial.github.io/sanssouci") + (synopsis "Post Hoc multiple testing inference") + (description + "The goal of sansSouci is to perform post hoc inference: in a multiple +testing context, sansSouci provides statistical guarantees on possibly +user-defined and/or data-driven sets of hypotheses.") + (license license:gpl3)))) + (define-public r-monocle3 (package (name "r-monocle3") |