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spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 5.81 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=qS2XbgYs; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 1E8F2FE34 X-Spam-Score: 5.81 X-Migadu-Scanner: scn0.migadu.com X-TUID: 5Bmbfndv8rhj diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..a78ceb2de5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,58 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(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") base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb -- 2.36.1