From 1edec0e8999cf4900fa0eddb4e11a790021a002c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 23:09:06 +0200 Subject: gnu: Add r-zinbwave. * gnu/packages/bioconductor.scm (r-zinbwave): New variable. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8ec7a6d90d..23a87c3dde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6629,6 +6629,39 @@ deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) +(define-public r-zinbwave + (package + (name "r-zinbwave") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zinbwave" version)) + (sha256 + (base32 + "0m5f0wrk6kg88m41cchjwi4ssi7kr3196m8h9hrhygak964nsd4q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-matrix" ,r-matrix) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-softimpute" ,r-softimpute) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/zinbwave") + (synopsis "Zero-inflated negative binomial model for RNA-seq data") + (description "This package implements a general and flexible zero-inflated +negative binomial model that can be used to provide a low-dimensional +representations of single-cell RNA-seq data. The model accounts for zero +inflation (dropouts), over-dispersion, and the count nature of the data. +The model also accounts for the difference in library sizes and optionally +for batch effects and/or other covariates, avoiding the need for pre-normalize +the data.") + (license license:artistic2.0))) + (define-public r-zfpkm (package (name "r-zfpkm") -- cgit v1.2.3