diff options
| -rw-r--r-- | gnu/packages/bioconductor.scm | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9517cee52e..d2a296ff66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -49,6 +49,7 @@ #: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 @@ and evaluate clustering results.") 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") |