Subject: bug#71339: closed ([PATCH] gnu: Add r-scent.)

From: [email-masked] (GNU bug Tracking System)
Date: Tue, 18 Jun 2024 07:28:02 +0000

Your bug report

#71339: [PATCH] gnu: Add r-scent.

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].

-- 
71339: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=71339
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: [PATCH] gnu: Add r-scent.
From: Ricardo Wurmus <[email-masked]>
To: [email-masked]
Date: Tue, 18 Jun 2024 09:27:34 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

Thanks for the patch.  Applied!

-- 
Ricardo

Subject: [PATCH] gnu: Add r-scent.
From: "Afkhami, Navid" <[email-masked]>
To: <[email-masked]>
Cc: "Afkhami, Navid" <[email-masked]>
Date: Mon, 3 Jun 2024 14:19:55 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/bioinformatics.scm (r-scent): New variable.

Change-Id: Ie517c0619683590f630013982e831fad528c1dea
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cecd94bbb7..cdda029809 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1171,6 +1171,43 @@ (define-public r-scenic
       ;; GPLv3.
       (license license:gpl3))))
 
+(define-public r-scent
+  (let ((commit "f01f18ac30f8a9bcf85b738c6c7815017e2c8ee5")
+        (revision "1"))
+    (package
+      (name "r-scent")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/immunogenomics/SCENT")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "18krksy8ac7yy8hghzaxscj91c61j195yg7j60zswdq97islvfzi"))))
+      (properties `((upstream-name . "SCENT")))
+      (build-system r-build-system)
+      (inputs (list bedtools))
+      (propagated-inputs (list r-boot
+                               r-data-table
+                               r-hmisc
+                               r-lme4
+                               r-mass
+                               r-matrix
+                               r-r-utils
+                               r-stringr))
+      (native-inputs (list r-knitr))
+      (home-page "https://github.com/immunogenomics/SCENT")
+      (synopsis
+       "Single-Cell enhancer target gene mapping for multimodal single-cell data")
+      (description
+       "This package contains functions for the SCENT algorithm.
+SCENT uses single-cell multimodal data and links ATAC-seq peaks
+to their target genes by modeling association between chromatin
+accessibility and gene expression across individual single cells.")
+      (license license:expat))))
+
 (define-public r-saige
   (let ((commit "c6717ba9c5a967bcf612e97566d845397b1b7167")
         (revision "1"))

base-commit: 1615084a9a4115d48b75b3db048761e7534efc87
-- 
2.34.1