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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2022-10-30 01:16:06 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-10-31 19:59:01 +0100 |
| commit | ae94d879a1179d372e68a9fe7df14311be7b9789 (patch) | |
| tree | eed66268cb64963aeef6f17109444b406a159fe8 /gnu/packages/bioconductor.scm | |
| parent | a8631c816d78ede76f279e288efbb284090f8c91 (diff) | |
gnu: Add r-decomptumor2sig.
* gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e4c8d9cdb5..80acaee764 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3253,6 +3253,49 @@ analysis results, users are possible to find the patients affected by the same mechanism based on the shared signatures.") (license license:gpl3))) +(define-public r-decomptumor2sig + (package + (name "r-decomptumor2sig") + (version "2.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "decompTumor2Sig" version)) + (sha256 + (base32 + "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6")))) + (properties `((upstream-name . "decompTumor2Sig"))) + (build-system r-build-system) + (inputs (list perl)) ;script/extractSpecColumns.pl + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-data-table + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gridextra + r-matrix + r-plyr + r-quadprog + r-readxl + r-s4vectors + r-summarizedexperiment + r-txdb-hsapiens-ucsc-hg19-knowngene + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://rmpiro.net/decompTumor2Sig/") + (synopsis "Decomposition of individual tumors into mutational signatures") + (description + "The package uses quadratic programming for signature refitting, i.e., to +decompose the mutation catalog from an individual tumor sample into a set of +given mutational signatures (either Alexandrov-model signatures or +Shiraishi-model signatures), computing weights that reflect the contributions +of the signatures to the mutation load of the tumor.") + (license license:gpl2))) + (define-public r-deconvr (package (name "r-deconvr") |