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07/08: gnu: Add r-pagoda2.
From: |
guix-commits |
Subject: |
07/08: gnu: Add r-pagoda2. |
Date: |
Wed, 1 Mar 2023 07:47:16 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 020e5ac362e3dbb578da40adeaa929a2f5fd3929
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Mon Feb 27 11:28:45 2023 +0100
gnu: Add r-pagoda2.
* gnu/packages/cran.scm (r-pagoda2): New variable.
---
gnu/packages/cran.scm | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d4acc8cfdc..5e69b7e3f6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2031,6 +2031,59 @@ consistent fashion. It seeks to combine functionality
from lower level
functions which can speed up workflow.")
(license license:gpl2)))
+(define-public r-pagoda2
+ (package
+ (name "r-pagoda2")
+ (version "1.0.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pagoda2" version))
+ (sha256
+ (base32 "18ip8j5l5c3hqw1xsf5wnyas55i2mhk09phy68kjkjdgcymmpg7c"))))
+ (properties `((upstream-name . "pagoda2")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-dendsort
+ r-drat
+ r-fastcluster
+ r-igraph
+ r-irlba
+ r-magrittr
+ r-mass
+ r-matrix
+ r-mgcv
+ r-n2r
+ r-plyr
+ r-r-utils
+ r-r6
+ r-rcpp
+ r-rcpparmadillo
+ r-rcppeigen
+ r-rcppprogress
+ r-rjson
+ r-rlang
+ r-rmtstat
+ r-rook
+ r-rtsne
+ r-sccore
+ r-urltools))
+ (home-page "https://github.com/kharchenkolab/pagoda2")
+ (synopsis "Single cell analysis and differential expression")
+ (description
+ "The package offers functions for analyzing and interactively exploring
+large-scale single-cell RNA-seq datasets. Pagoda2 primarily performs
+normalization and differential gene expression analysis, with an interactive
+application for exploring single-cell RNA-seq datasets. It performs basic
+tasks such as cell size normalization, gene variance normalization, and can be
+used to identify subpopulations and run differential expression within
+individual samples. pagoda2 was written to rapidly process modern large-scale
+scRNAseq datasets of approximately 1e6 cells. The companion web application
+allows users to explore which gene expression patterns form the different
+subpopulations within your data. The package also serves as the primary
+method for preprocessing data for conos.")
+ (license license:gpl3)))
+
(define-public r-pals
(package
(name "r-pals")
- branch master updated (2eb750ab1f -> 1fb43d1d19), guix-commits, 2023/03/01
- 02/08: gnu: Add r-n2r., guix-commits, 2023/03/01
- 06/08: gnu: Add r-dendsort., guix-commits, 2023/03/01
- 01/08: gnu: Add r-rcppspdlog., guix-commits, 2023/03/01
- 05/08: gnu: Add r-drat., guix-commits, 2023/03/01
- 07/08: gnu: Add r-pagoda2.,
guix-commits <=
- 03/08: gnu: Add r-sccore., guix-commits, 2023/03/01
- 04/08: gnu: Add r-leidenalg., guix-commits, 2023/03/01
- 08/08: gnu: Add r-conos., guix-commits, 2023/03/01