GNU bug report logs - #61252
[PATCH 3/3] gnu: Add r-dorothea.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: bug#61252: closed ([PATCH 3/3] gnu: Add r-dorothea.)
Date: Fri, 03 Feb 2023 15:51:02 +0000

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Your bug report

#61252: [PATCH 3/3] gnu: Add r-dorothea.

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 61252 <at> debbugs.gnu.org.

-- 
61252: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=61252
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 61252-done <at> debbugs.gnu.org
Subject: [PATCH 3/3] gnu: Add r-dorothea.
Date: Fri, 03 Feb 2023 16:49:38 +0100

Thanks for the patch!

Since this depends on r-viper, which is nonfree I cannot add this
package to Guix.  I have instead pushed it to the channel
“guix-science-nonfree”.

-- 
Ricardo

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH 3/3] gnu: Add r-dorothea.
Date: Fri, 3 Feb 2023 13:18:54 +0100

* gnu/packages/bioconductor.scm (r-dorothea): New variable.
---
 gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 521d6c00be..0786160b5e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -466,6 +466,31 @@ (define-public r-bsgenome-mmusculus-ucsc-mm10
 in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-dorothea
+  (package
+    (name "r-dorothea")
+    (version "1.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "dorothea" version
+                                     'experiment))
+              (sha256
+               (base32
+                "05vkb5mash2m8p6njk842sy5pz7vblrm8n9bphqbslm86kld5n92"))))
+    (properties `((upstream-name . "dorothea")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bcellviper r-dplyr r-magrittr r-viper))
+    (native-inputs (list r-knitr))
+    (home-page "https://saezlab.github.io/dorothea/")
+    (synopsis "Collection of human and mouse TF regulons")
+    (description
+     "DoRothEA is a gene regulatory network containing signed transcription factor.
+DoRothEA regulons, the collection of a TF andits transcriptional targets,
+were curated and collected from different types ofevidence for both human
+and mouse.  A confidence level was assigned to each TF-target interaction
+based on the number of supporting evidence.")
+    (license license:gpl3)))
+
 (define-public r-genomeinfodbdata
   (package
     (name "r-genomeinfodbdata")
-- 
2.34.1

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