From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <58879@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig.
Date: Sun, 30 Oct 2022 01:16:06 +0200 [thread overview]
Message-ID: <20221029231608.13909-3-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20221029231608.13909-1-madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable.
---
gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 809ba69bc3..7f6ba37bf8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3150,6 +3150,49 @@ (define-public r-decomplexdisease
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")
--
2.38.0
next prev parent reply other threads:[~2022-10-29 23:18 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-10-29 23:09 [bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam MadalinIonel.Patrascu
2022-10-29 23:16 ` [bug#58879] [PATCH 1/5] gnu: Add r-deco Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease Mădălin Ionel Patrașcu
2022-10-29 23:16 ` Mădălin Ionel Patrașcu [this message]
2022-10-29 23:16 ` [bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq Mădălin Ionel Patrașcu
2022-10-29 23:16 ` [bug#58879] [PATCH 5/5] gnu: Add r-decontam Mădălin Ionel Patrașcu
2022-10-31 19:06 ` bug#58879: [PATCH 1/5] gnu: Add r-deco Ricardo Wurmus
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