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author | Simon Tournier <zimon.toutoune@gmail.com> | 2023-01-17 18:30:41 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2023-01-20 10:44:28 +0100 |
commit | c31d8adcb0e4d5780583f26d51a1b4d3552783f2 (patch) | |
tree | fad17bf099f2c7e73a2140f10d60c4db9c6be11d /gnu/packages/bioconductor.scm | |
parent | 2a2165a18e0bb915cdb01f4831abb669f2aa8585 (diff) | |
download | guix-c31d8adcb0e4d5780583f26d51a1b4d3552783f2.tar.gz guix-c31d8adcb0e4d5780583f26d51a1b4d3552783f2.zip |
gnu: Add r-numbat.
* gnu/packages/bioconductor.scm (r-numbat): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r-- | gnu/packages/bioconductor.scm | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6d16a99c36..f1760b2007 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6750,6 +6750,73 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (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 (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It 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. It 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). It 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 + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") |