GNU bug report logs - #55145
[PATCH] gnu: Add r-agdex.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#55145: closed ([PATCH] gnu: Add r-agdex.)
Date: Wed, 27 Apr 2022 14:28:02 +0000

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Your message dated Wed, 27 Apr 2022 16:27:27 +0200
with message-id <87bkwm4n4z.fsf <at> elephly.net>
and subject line Re: [bug#55145] [PATCH] gnu: Add r-agdex.
has caused the debbugs.gnu.org bug report #55145,
regarding [PATCH] gnu: Add r-agdex.
to be marked as done.

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add r-agdex.
Date: Wed, 27 Apr 2022 13:20:14 +0200

* gnu/packages/bioconductor.scm (r-agdex): 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 67ee6079c6..1de7f83845 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1664,6 +1664,33 @@ (define-public r-adamgui
 the @code{GFAGpathUi} function.")
     (license license:gpl2+)))
 
+(define-public r-agdex
+  (package
+    (name "r-agdex")
+    (version "1.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AGDEX" version))
+              (sha256
+               (base32
+                "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64"))))
+    (properties `((upstream-name . "AGDEX")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-gseabase))
+    (home-page "https://bioconductor.org/packages/AGDEX")
+    (synopsis
+     "Evaluate agreement of differential expression for cross-species genomics")
+    (description
+     "The objective of @code{AGDEX} is to evaluate whether the results of a pair
+of two-group differential expression analysis comparisons show a level of
+agreement that is greater than expected if the group labels for each two-group
+comparison are randomly assigned.  The agreement is evaluated for the entire
+transcriptome and (optionally) for a collection of pre-defined gene-sets.
+Additionally, the procedure performs permutation-based differential expression
+and meta analysis at both gene and gene-set levels of the data from each
+experiment.")
+    (license license:gpl2+)))
+
 (define-public r-aneufinder
   (package
     (name "r-aneufinder")

base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76
-- 
2.34.0

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 55145-done <at> debbugs.gnu.org
Subject: Re: [bug#55145] [PATCH] gnu: Add r-agdex.
Date: Wed, 27 Apr 2022 16:27:27 +0200

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

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

Applied, thanks!

-- 
Ricardo

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