nafkhamdc wrote 1 years ago
(address . guix-patches@gnu.org)(name . nafkhamdc)(address . navid.afkhami@mdc-berlin.de)
79a84f556ed434e7a51f4fb87872872ef719719b.1704891744.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-dsb): New variable.
Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd
---
gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
Toggle diff (43 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7af5c42ce..7c4272f8be 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5599,6 +5599,34 @@ (define-public r-dropletutils
pseudo-cells, and downsampling of the count matrix.")
(license license:gpl3)))
+;; This is a CRAN package, but it depends on r-limma from Bioconductor.
+(define-public r-dsb
+ (package
+ (name "r-dsb")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dsb" version))
+ (sha256
+ (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2"))))
+ (properties `((upstream-name . "dsb")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-limma r-magrittr r-mclust))
+ (native-inputs (list r-knitr r-rmarkdown))
+ (home-page "https://github.com/niaid/dsb")
+ (synopsis
+ "Normalize & denoise droplet single cell protein data (CITE-Seq)")
+ (description
+ "R-dsb improves protein expression analysis in droplet-based single-cell studies.
+The package specifically addresses noise in raw protein UMI counts from methods like
+CITE-seq. It identifies and removes two main sources of noise—protein-specific noise
+from unbound antibodies and droplet/cell-specific noise. The package is applicable to
+various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform
+data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor,
+and using dsb in Python.")
+ (license license:cc0)))
+
(define-public r-dss
(package
(name "r-dss")
base-commit: 537768018ee03a6a9a5562022a16b47ac287d131
--
2.34.1