From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <68056@debbugs.gnu.org>
Subject: [bug#68056] [PATCH 2/3] gnu: Add r-stacas.
Date: Wed, 27 Dec 2023 11:02:35 +0100 [thread overview]
Message-ID: <f8637e701714926d5ee5265758fe977dad296d0e.1703671356.git.madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <dce9fb4afc7cc569984b722a43f51388bbb5a69f.1703671356.git.madalinionel.patrascu@mdc-berlin.de>
* 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
next prev parent reply other threads:[~2023-12-27 10:04 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-12-27 9:58 [bug#68056] [PATCH] gnu: Add r-scgate, r-stacas and r-projectils Mădălin Ionel Patrașcu
2023-12-27 10:02 ` [bug#68056] [PATCH 1/3] gnu: Add r-scgate Mădălin Ionel Patrașcu
2023-12-27 10:02 ` Mădălin Ionel Patrașcu [this message]
2023-12-27 10:02 ` [bug#68056] [PATCH 3/3] gnu: Add r-projectils Mădălin Ionel Patrașcu
2024-01-30 16:27 ` bug#68056: [PATCH] gnu: Add r-scgate, r-stacas and r-projectils Ricardo Wurmus
2024-01-30 17:05 ` [bug#68056] " Ricardo Wurmus
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