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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=YVDxlLcm; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.18 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=YVDxlLcm; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: CF0A88BFA X-Spam-Score: 7.18 X-Migadu-Scanner: scn1.migadu.com X-TUID: hrojnluZz4Uc * gnu/packages/bioconductor.scm (r-infercnv): New variable. --- gnu/packages/bioconductor.scm | 60 +++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 31484799b2..e9bfbed9b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -49,6 +49,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) + #:use-module (gnu packages python) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) @@ -2647,6 +2648,65 @@ (define-public r-ideoviz arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-infercnv + (package + (name "r-infercnv") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "infercnv" version)) + (sha256 + (base32 + "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl")))) + (properties `((upstream-name . "infercnv"))) + (build-system r-build-system) + (inputs (list python)) + (propagated-inputs + (list r-ape + r-argparse + r-biocgenerics + r-catools + r-coda + r-coin + r-digest + r-doparallel + r-dplyr + r-edger + r-fastcluster + r-fitdistrplus + r-foreach + r-futile-logger + r-future + r-ggplot2 + r-gplots + r-gridextra + r-hiddenmarkov + r-leiden + r-matrix + r-paralleldist + r-phyclust + r-rann + r-rcolorbrewer + r-reshape + r-rjags + r-singlecellexperiment + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/broadinstitute/inferCNV/wiki") + (synopsis "Infer copy number variation from single-cell RNA-Seq data") + (description + "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify +evidence for somatic large-scale chromosomal copy number alterations, such as gains +or deletions of entire chromosomes or large segments of chromosomes. This is done +by exploring expression intensity of genes across positions of a tumor genome in +comparison to a set of reference \"normal\" cells. A heatmap is generated +illustrating the relative expression intensities across each chromosome, and it +often becomes readily apparent as to which regions of the tumor genome are +over-abundant or less-abundant as compared to that of normal cells.") + (license license:bsd-3))) + (define-public r-iranges (package (name "r-iranges") -- 2.37.1