Subject: [PATCH 2/3] gnu: Add r-stacas.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Wed, 27 Dec 2023 11:02:35 +0100

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

Change-Id: I258a315465ed88b8013d26a36718250c950aa107
---
 gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d572980965..d736abe07e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1069,6 +1069,42 @@ (define-public r-singlet
 similar.")
       (license license:gpl2+))))
 
+(define-public r-stacas
+  (package
+    (name "r-stacas")
+    (version "2.2.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/carmonalab/STACAS")
+              (commit version)))
+        (file-name (git-file-name name version))
+        (sha256
+        (base32 "13i0h5i6vlbrb8ndq9gr81560z9d74b2c7m3rjfzls01irjza9hm"))))
+    (properties `((upstream-name . "STACAS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocneighbors
+           r-biocparallel
+           r-ggplot2
+           r-ggridges
+           r-pbapply
+           r-r-utils
+           r-seurat))
+    (home-page "https://github.com/carmonalab/STACAS")
+    (synopsis "Sub-type anchoring correction for alignment in Seurat")
+    (description
+      "This package implements methods for batch correction and integration of
+scRNA-seq datasets, based on the Seurat anchor-based integration framework.  In
+particular, STACAS is optimized for the integration of heterogenous datasets with
+only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with
+CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods
+would tend to over-correct biological differences.  The 2.0 version of the package
+allows the users to incorporate explicit information about cell-types in order
+to assist the integration process.")
+    (license license:gpl3)))
+
 (define-public r-stringendo
   (let ((commit "15594b1bba11048a812874bafec0eea1dcc8618a")
         (revision "1"))
-- 
2.41.0