GNU bug report logs - #53349
[PATCH 0/9] Add 2 bioinformatics R packages

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Message #17 received at 53349 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 53349 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/9] gnu: Add r-jetset.
Date: Tue, 18 Jan 2022 18:54:11 +0100

* gnu/packages/bioconductor.scm (r-jetset): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7194e8b0e7..935c958cd0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1965,6 +1965,33 @@ (define-public r-deconstructsigs
 closely reconstructs the mutational profile.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-jetset
+  (package
+    (name "r-jetset")
+    (version "3.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jetset" version))
+       (sha256
+        (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
+    (properties `((upstream-name . "jetset")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+    (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
+    (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
+    (description
+     "This package provides a one-to-one mapping from gene to \"best\" probe
+set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
+hgu133plus2, and u133x3p.  On Affymetrix gene expression microarrays, a single
+gene may be measured by multiple probe sets.  This can present a mild
+conundrum when attempting to evaluate a gene \"signature\" that is defined by
+gene names rather than by specific probe sets.  This package also includes the
+pre-calculated probe set quality scores that were used to define the
+mapping.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages.
 (define-public r-nmf
   (package
-- 
2.34.0

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