From af81591375ac5cc58fbf619a0eaa80a4245e1a00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 7 Sep 2021 11:44:13 +0200 Subject: gnu: Add r-bgeecall. * gnu/packages/bioconductor.scm (r-bgeecall): New variable. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2d687a5e6..6140d2987e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13766,6 +13766,42 @@ and can also be used to predict missing values in any other matrix containing real numbers.") (license license:gpl3))) +(define-public r-bgeecall + (package + (name "r-bgeecall") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeCall" version)) + (sha256 + (base32 + "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + (properties `((upstream-name . "BgeeCall"))) + (build-system r-build-system) + (propagated-inputs + `(("kallisto" ,kallisto) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-jsonlite" ,r-jsonlite) + ("r-rhdf5" ,r-rhdf5) + ("r-rslurm" ,r-rslurm) + ("r-rtracklayer" ,r-rtracklayer) + ("r-sjmisc" ,r-sjmisc) + ("r-tximport" ,r-tximport))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/BgeeDB/BgeeCall") + (synopsis "RNA-Seq present/absent gene expression calls generation") + (description + "BgeeCall allows to generate present/absent gene expression calls without +using an arbitrary cutoff like TPM<1. Calls are generated based on reference +intergenic sequences. These sequences are generated based on expression of +all RNA-Seq libraries of each species integrated in Bgee.") + (license license:gpl3))) + (define-public r-tximeta (package (name "r-tximeta") -- cgit v1.2.3