GNU bug report logs - #45283
[PATCH] gnu: Add r-gagedata.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: rekado <at> elephly.net, Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-gagedata.
Date: Wed, 16 Dec 2020 23:17:01 +0100

* gnu/packages/bioconductor.scm (r-gagedata): New variable.
---
 gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 85ee56c539..36274d0b39 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9187,3 +9187,29 @@ CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
 preprocessing of cytometry data, including i) normalization using bead
 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
     (license license:gpl2+)))
+
+(define-public r-gagedata
+  (package
+    (name "r-gagedata")
+    (version "2.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gageData" version 'experiment))
+       (sha256
+        (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
+    (properties `((upstream-name . "gageData")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/gageData")
+    (synopsis "Auxillary data for gage package")
+    (description
+     "This is a supportive data package for the software package @code{gage}.
+However, the data supplied here are also useful for gene set or pathway
+analysis or microarray data analysis in general.  In this package, we provide
+two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
+BMP6 (originally published as an demo dataset for GAGE, also registered as
+GSE13604 in GEO).  This package also includes commonly used gene set data based
+on KEGG pathways and GO terms for major research species, including human,
+mouse, rat and budding yeast.  Mapping data between common gene IDs for budding
+yeast are also included.")
+    (license license:gpl2+)))
-- 
2.29.2

Message #10 received at 45283-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 45283-done <at> debbugs.gnu.org
Subject: Re: [PATCH] gnu: Add r-gagedata.
Date: Thu, 17 Dec 2020 12:33:03 +0100

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-gagedata): New variable.

Applied, thanks!

-- 
Ricardo

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