Subject: bug#55145: closed (Re: [bug#55145] [PATCH] gnu: Add r-agdex.)

From: [email-masked] (GNU bug Tracking System)
Date: Wed, 27 Apr 2022 14:28:02 +0000

Your bug report

#55145: [PATCH] gnu: Add r-agdex.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
55145: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=55145
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#55145] [PATCH] gnu: Add r-agdex.
From: Ricardo Wurmus <[email-masked]>
To: Mădălin Ionel Patrașcu<[email-masked]>
Cc: [email-masked]
Date: Wed, 27 Apr 2022 16:27:27 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

Mădălin Ionel Patrașcu <[email-masked]> writes:

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

Applied, thanks!

-- 
Ricardo

Subject: [PATCH] gnu: Add r-agdex.
From: Mădălin Ionel Patrașcu<[email-masked]>
To: <[email-masked]>
Date: Wed, 27 Apr 2022 13:20:14 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

* 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