NMF: Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

Provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

Version:	0.28
Depends:	R (≥ 3.0.0), methods, utils, registry, rngtools (≥ 1.2.3), cluster
Imports:	graphics, stats, stringr (≥ 1.0.0), digest, grid, grDevices, gridBase, colorspace, RColorBrewer, foreach, doParallel, ggplot2, reshape2, Biobase, codetools, BiocManager
Suggests:	fastICA, doMPI, bigmemory (≥ 4.2), synchronicity (≥ 1.3.2), corpcor, xtable, devtools, knitr, RUnit
Published:	2024-08-22
DOI:	10.32614/CRAN.package.NMF
Author:	Renaud Gaujoux [aut], Cathal Seoighe [aut], Nicolas Sauwen [cre]
Maintainer:	Nicolas Sauwen <nicolas.sauwen at openanalytics.eu>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	http://renozao.github.io/NMF/
NeedsCompilation:	yes
Citation:	NMF citation info
Materials:	README NEWS
CRAN checks:	NMF results

Documentation:

Reference manual:	NMF.pdf
Vignettes:	An introduction to the package NMF (source, R code) NMF: generating heatmaps (source, R code)

Downloads:

Package source:	NMF_0.28.tar.gz
Windows binaries:	r-devel: NMF_0.28.zip, r-release: NMF_0.28.zip, r-oldrel: NMF_0.28.zip
macOS binaries:	r-release (arm64): NMF_0.28.tgz, r-oldrel (arm64): NMF_0.28.tgz, r-release (x86_64): NMF_0.28.tgz, r-oldrel (x86_64): NMF_0.28.tgz
Old sources:	NMF archive

Reverse dependencies:

Reverse depends:	fabisearch, funOmics, InterSIM, IntNMF, musicatk, MutationalPatterns, signeR, SomaticSignatures, SparseSignatures
Reverse imports:	clusterExperiment, DBNMFrank, debCAM, diceR, funOmics, hNMF, miRSM, pcaExplorer, projectR, SCdeconR, scITD, shattering, sigminer, SomaticSignatures, spectralAnalysis, SpNMF, SPOTlight
Reverse suggests:	AUCell, cola, crassmat, dimRed, Evacluster, iTOP, maftools, MAST, mia, mlr3pipelines, scone
Reverse enhances:	fdm2id

Linking:

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