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Change-Id: I34b91da1ae177bd37cfa548c5f6fede453f29bcd --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) base-commit: 537768018ee03a6a9a5562022a16b47ac287d131 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")