diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2023-07-12 21:34:07 +0200 |
---|---|---|
committer | Ricardo Wurmus <rekado@elephly.net> | 2023-07-12 21:34:07 +0200 |
commit | 2794caed7c813f2ec4249236de36eaccafee8361 (patch) | |
tree | 8c073428e5d7f6b9f808b122893cb561e934aa78 /gnu/packages/bioinformatics.scm | |
parent | 3b524cde7115a6e89a438c1fd230093e6f30442f (diff) |
gnu: Add r-numbat.
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 72 |
1 files changed, 72 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9342c44474..341731d066 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -875,6 +875,78 @@ attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.") (license license:gpl3)))) +(define-public r-numbat + (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295") + (revision "1")) + (package + (name "r-numbat") + (version (git-version "1.3.2-1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kharchenkolab/numbat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0wa2cz5iy570r2a57bd74jramxayvfhmxznb0vq4vyk1ia8l5jd1")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs + (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-Aware CNV Analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. numbat integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. numbat can be used +to: + +@enumerate +@item detect allele-specific copy number variations from single-cells; +@item differentiate tumor versus normal cells in the tumor microenvironment; +@item infer the clonal architecture and evolutionary history of profiled +tumors. +@end enumerate + +numbat does not require tumor/normal-paired DNA or genotype data, but operates +solely on the donor scRNA-data data (for example, 10x Cell Ranger output).") + (license license:expat)))) + (define-public r-p2data (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c") (revision "1")) |