diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 129 |
1 files changed, 128 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6a8216ccb..dfb0fe6d5a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -28,7 +28,8 @@ #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages graph) - #:use-module (gnu packages statistics)) + #:use-module (gnu packages statistics) + #:use-module (gnu packages web)) (define-public r-bsgenome-dmelanogaster-ucsc-dm6 (package @@ -167,6 +168,35 @@ Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default." ) (license license:artistic2.0))) +(define-public r-genelendatabase + (package + (name "r-genelendatabase") + (version "1.16.0") + (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://bioconductor.org/packages/" + "release/data/experiment/src/contrib" + "/geneLenDataBase_" version ".tar.gz")) + (sha256 + (base32 + "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5")))) + (properties + `((upstream-name . "geneLenDataBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rtracklayer" ,r-rtracklayer) + ("r-genomicfeatures" ,r-genomicfeatures))) + (home-page "https://bioconductor.org/packages/geneLenDataBase/") + (synopsis "Lengths of mRNA transcripts for a number of genomes") + (description + "This package provides the lengths of mRNA transcripts for a number of +genomes and gene ID formats, largely based on the UCSC table browser.") + (license license:lgpl2.0+))) + + (define-public r-hpar (package (name "r-hpar") @@ -675,3 +705,100 @@ experiments.") such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics.") (license license:gpl3))) + +(define-public r-ctc + (package + (name "r-ctc") + (version "1.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ctc" version)) + (sha256 + (base32 + "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9")))) + (build-system r-build-system) + (propagated-inputs `(("r-amap" ,r-amap))) + (home-page "https://bioconductor.org/packages/ctc/") + (synopsis "Cluster and tree conversion") + (description + "This package provides tools for exporting and importing classification +trees and clusters to other programs.") + (license license:gpl2))) + +(define-public r-goseq + (package + (name "r-goseq") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "goseq" version)) + (sha256 + (base32 + "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biasedurn" ,r-biasedurn) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genelendatabase" ,r-genelendatabase) + ("r-go-db" ,r-go-db) + ("r-mgcv" ,r-mgcv))) + (home-page "https://bioconductor.org/packages/goseq/") + (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") + (description + "This package provides tools to detect Gene Ontology and/or other user +defined categories which are over/under represented in RNA-seq data.") + (license license:lgpl2.0+))) + +(define-public r-glimma + (package + (name "r-glimma") + (version "1.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Glimma" version)) + (sha256 + (base32 + "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s")))) + (properties `((upstream-name . "Glimma"))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-jsonlite" ,r-jsonlite) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/Shians/Glimma") + (synopsis "Interactive HTML graphics") + (description + "This package generates interactive visualisations for analysis of +RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an +HTML page. The interactions are built on top of the popular static +representations of analysis results in order to provide additional +information.") + (license license:lgpl3))) + +(define-public r-rots + (package + (name "r-rots") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ROTS" version)) + (sha256 + (base32 + "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3")))) + (properties `((upstream-name . "ROTS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-rcpp" ,r-rcpp))) + (home-page "https://bioconductor.org/packages/ROTS/") + (synopsis "Reproducibility-Optimized Test Statistic") + (description + "This package provides tools for calculating the +@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing +in omics data.") + (license license:gpl2+))) |