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02/02: gnu: Add r-amaretto.
From: |
guix-commits |
Subject: |
02/02: gnu: Add r-amaretto. |
Date: |
Thu, 30 Jun 2022 10:20:18 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit c6d792f34cc1af122d9089451a2b784d405d1923
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Fri Jun 17 11:29:29 2022 +0200
gnu: Add r-amaretto.
* gnu/packages/bioconductor.scm (r-amaretto): New variable.
---
gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 20f277b119..28000c70f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2011,6 +2011,58 @@ conditions or various species. @code{AMOUNTAIN} aims to
search active modules
in multi-layer WGCN using a continuous optimization approach.")
(license license:gpl2+)))
+(define-public r-amaretto
+ (package
+ (name "r-amaretto")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AMARETTO" version))
+ (sha256
+ (base32
+ "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
+ (properties `((upstream-name . "AMARETTO")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocfilecache
+ r-callr
+ r-circlize
+ r-complexheatmap
+ r-curatedtcgadata
+ r-doparallel
+ r-dplyr
+ r-dt
+ r-foreach
+ r-ggplot2
+ r-glmnet
+ r-gridextra
+ r-httr
+ r-impute
+ r-knitr
+ r-limma
+ r-matrix
+ r-matrixstats
+ r-multiassayexperiment
+ r-rcpp
+ r-readr
+ r-reshape2
+ r-rmarkdown
+ r-tibble))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/AMARETTO")
+ (synopsis "Regulatory network inference and driver gene evaluation")
+ (description
+ "This package @code{AMARETTO} represents an algorithm that integrates copy
+number, DNA methylation and gene expression data to identify a set of driver
+genes by analyzing cancer samples and connects them to clusters of co-expressed
+genes, which we define as modules. @code{AMARETTO} can be applied in a
pancancer
+setting to identify cancer driver genes and their modules on multiple cancer
+sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
+and EMT, and modules that accurately predict survival and molecular subtypes.
+This allows @code{AMARETTO} to identify novel cancer driver genes directing
+canonical cancer pathways.")
+ (license license:asl2.0)))
+
(define-public r-aneufinder
(package
(name "r-aneufinder")