GNU bug report logs - #32682
[PATCH] gnu: Add r-absfiltergsea.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Leo Famulari <leo <at> famulari.name>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#32682: closed ([PATCH] gnu: Add r-absfiltergsea.)
Date: Tue, 02 Oct 2018 20:25:02 +0000

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Your message dated Tue, 2 Oct 2018 16:24:16 -0400
with message-id <20181002202416.GB20264 <at> jasmine.lan>
and subject line Re: [bug#32682] [PATCH] gnu: Add r-absfiltergsea.
has caused the debbugs.gnu.org bug report #32682,
regarding [PATCH] gnu: Add r-absfiltergsea.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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32682: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=32682
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From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add r-absfiltergsea.
Date: Mon, 10 Sep 2018 16:05:41 +0200

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6580cac53..9c01cb86f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13504,3 +13504,30 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
        (list
         license:expat                   ;license for gffcompare
         license:artistic2.0)))))        ;license for gclib
+
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))
-- 
2.17.1

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From: Leo Famulari <leo <at> famulari.name>
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 32682-done <at> debbugs.gnu.org
Subject: Re: [bug#32682] [PATCH] gnu: Add r-absfiltergsea.
Date: Tue, 2 Oct 2018 16:24:16 -0400

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On Mon, Sep 10, 2018 at 04:05:41PM +0200, pimi wrote:
> gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.

Thanks! Pushed as 0f1622220a39a620854b0a268793e262746d460a

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