GNU bug report logs - #53349
[PATCH 0/9] Add 2 bioinformatics R packages

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Message #32 received at 53349 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 53349 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 8/9] gnu: Add r-icellnet.
Date: Tue, 18 Jan 2022 18:54:17 +0100

* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
---
 gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6caeec80f7..b2bd7fbbc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,7 @@
 ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki <at> gmail.com>
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
-;;; Copyright © 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -7771,6 +7771,50 @@ (define-public r-archr
        "This package is designed to streamline scATAC analyses in R.")
       (license license:gpl2+))))
 
+(define-public r-icellnet
+  ;; v1.0 tagged in 2020, last commit contains many fixes.
+  ;; DESCRIPTION says Version: 0.0.0.9000.
+  (let ((commit "b9c05488fb8b5ea69bd560018966eaf4e25f82a")
+        (revision "0"))
+    (package
+      (name "r-icellnet")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/soumelis-lab/ICELLNET")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0cld7d6xqnvd0zpcpg3sx73an6vdc9divzywgnn6zxnqcd987cnw"))))
+      (build-system r-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'enter-dir
+             (lambda _ (chdir "icellnet"))))))
+      (propagated-inputs
+       (list r-annotationdbi
+             r-data-table
+             r-dplyr
+             r-ggplot2
+             r-hgu133plus2-db
+             r-jetset
+             r-psych
+             r-reshape2
+             r-rlist))
+      (home-page "https://github.com/soumelis-lab/ICELLNET")
+      (synopsis "Transcriptomic-based framework to dissect cell communication")
+      (description "This packages provides a a transcriptomic-based framework
+to dissect cell communication in a global manner.  It integrates an original
+expert-curated database of ligand-receptor interactions taking into account
+multiple subunits expression.  Based on transcriptomic profiles (gene
+expression), this package allows to compute communication scores between cells
+and provides several visualization modes that can be helpful to dig into
+cell-cell interaction mechanism and extend biological knowledge.")
+      (license license:gpl3))))
+
 (define-public r-scde
   (package
     (name "r-scde")
-- 
2.34.0

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