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A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Version: | 0.6.2 |
Depends: | R (≥ 4.3.0) |
Imports: | RcppML, Matrix, stats, methods, utils, Seurat (≥ 4.3.0), cluster, lsa, irlba, pheatmap, dendextend, viridis |
Suggests: | knitr, rmarkdown, fgsea, msigdbr |
Published: | 2024-11-12 |
DOI: | 10.32614/CRAN.package.GeneNMF |
Author: | Massimo Andreatta [aut, cre], Santiago Carmona [aut] |
Maintainer: | Massimo Andreatta <massimo.andreatta at unil.ch> |
BugReports: | https://github.com/carmonalab/GeneNMF/issues |
License: | GPL-3 |
URL: | https://github.com/carmonalab/GeneNMF |
NeedsCompilation: | no |
Materials: | README NEWS |
CRAN checks: | GeneNMF results |
Reference manual: | GeneNMF.pdf |
Vignettes: |
Index of GeneNMF vignettes (source) |
Package source: | GeneNMF_0.6.2.tar.gz |
Windows binaries: | r-devel: GeneNMF_0.6.2.zip, r-release: GeneNMF_0.6.2.zip, r-oldrel: GeneNMF_0.6.2.zip |
macOS binaries: | r-release (arm64): GeneNMF_0.6.2.tgz, r-oldrel (arm64): GeneNMF_0.6.2.tgz, r-release (x86_64): GeneNMF_0.6.2.tgz, r-oldrel (x86_64): GeneNMF_0.6.2.tgz |
Old sources: | GeneNMF archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.