Algorithms and framework for Nonnegative Matrix Factorization
(NMF).
c( person("Renaud", "Gaujoux", role=c('aut', 'cre'),
email='renaud@mancala.cbio.uct.ac.za') , person("Cathal",
"Seoighe", role='ths') , person("P.", "Brunet", role = "ctb",
comment='method: brunet (Matlab original version)') ,
person("H.", "Kim", role = "ctb", comment='methods: snmf/r(l)
(Matlab original version)') )
This package provides a framework to perform Non-negative
Matrix Factorization (NMF). It 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.
R (>= 2.15.2), methods, stats, pkgmaker (>= 0.15.2), rngtools,
registry, digest, grid
graphics, rngtools, stringr, grDevices, gridBase, colorspace,
RColorBrewer, iterators, foreach, doParallel
RcppOctave (>= 0.8.12), Biobase, fastICA, doMPI, bigmemory
(>= 4.2), synchronicity, corpcor, xtable, devtools, knitr,
RUnit, mail
'rmatrix.R' 'nmf-package.R' 'utils.R' 'simulation.R'
'versions.R' 'colorcode.R' 'options.R' 'algorithmic.R'
'atracks.R' 'grid.R' 'aheatmap.R' 'NMF-class.R'
'extractFeatures.R' 'setNMFClass.R' 'NMFstd-class.R'
'fixed-terms.R' 'NMFOffset-class.R' 'NMFns-class.R'
'nmfModel.R' 'NMFfit-class.R' 'rnmf.R' 'heatmaps.R'
'NMFSet-class.R' 'registry.R' 'NMFStrategy-class.R'
'NMFStrategyFunction-class.R' 'NMFStrategyIterative-class.R'
'NMFStrategyOctave-class.R' 'registry-algorithms.R'
'algorithms-base.R' 'algorithms-brunet.R' 'NMFSeed-class.R'
'registry-seed.R' 'seed-base.R' 'parallel.R' 'nmf.R'
'Bioc-layer.R' 'transforms.R' 'NMFplots.R' 'algorithms-lnmf.R'
'algorithms-lsnmf.R' 'algorithms-pe-nmf.R' 'algorithms-snmf.R'
'algorithms-siNMF.R' 'seed-ica.R' 'seed-nndsvd.R' 'data.R'
'tests.R'

R (>= 2.15.2), methods, stats, pkgmaker (>= 0.16), rngtools,
registry, digest, grid

R (>= 2.15.2), methods, utils, stats, pkgmaker (>= 0.16),
rngtools, registry, digest, grid