diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dcce8a69ea4..d93c12e2a62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11926,6 +11926,50 @@ you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.") (license license:expat))) +(define-public r-recount + (package + (name "r-recount") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "recount" version)) + (sha256 + (base32 "0i512z370hrpgyddvgfd9mvcd0lhldbcs047q39brcf436a6glgs")))) + (properties `((upstream-name . "recount"))) + (build-system r-build-system) + ;; 3 tests attempt to download data. + (arguments (list #:tests? #false)) + (propagated-inputs (list r-biocparallel + r-derfinder + r-downloader + r-genomeinfodb + r-genomicranges + r-geoquery + r-iranges + r-rcurl + r-rentrez + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr r-testthat)) + (home-page "https://github.com/leekgroup/recount") + (synopsis "Explore and download data from the recount project") + (description + "Explore and download data from the recount project available at +https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you +can download @code{RangedSummarizedExperiment} objects at the gene, exon or +exon-exon junctions level, the raw counts, the phenotype metadata used, the +urls to the sample coverage @code{bigWig} files or the mean coverage +@code{bigWig} file for a particular study. The +@code{RangedSummarizedExperiment} objects can be used by different packages +for performing differential expression analysis. Using +http://bioconductor.org/packages/derfinder you can perform annotation-agnostic +differential expression analyses with the data from the recount project as +described at +@url{https://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html}.") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner")