Files in NMF
Algorithms and Framework for Nonnegative Matrix Factorization (NMF)

TODO
inst
inst/CITATION
inst/REFERENCES.bib
inst/tests
inst/tests/runit.NMFfit-class.r inst/tests/runit.interface.r inst/tests/runit.aheatmap.R inst/tests/runit.NMFSet.r inst/tests/runit.bioc.r inst/tests/runit.NMFclass.r inst/tests/runit.distance.r inst/tests/runit.utils.r inst/tests/runit.NMFStrategy-class.r inst/tests/runit.parallel.r inst/tests/runit.options.r inst/tests/runit.algorithms.r inst/tests/runit.seed.r
inst/scripts
inst/scripts/report.Rmd inst/scripts/grid.R
inst/doc
inst/doc/heatmaps.Rnw
inst/doc/NMF-unitTests.Rnw
inst/doc/NMF-vignette.R inst/doc/NMF-unitTests.R inst/doc/NMF-unitTests.pdf inst/doc/consensus.pdf inst/doc/NMF-vignette.pdf inst/doc/heatmaps.pdf
inst/doc/NMF-vignette.Rnw
inst/doc/heatmaps.R
inst/m-files
inst/m-files/brunet.R
inst/m-files/brunet-run.m
inst/m-files/brunet.m
tests
tests/doRUnit.R
src
src/divergence.cpp
src/euclidean.cpp
src/utils.cpp
src/distance.cpp
NAMESPACE
demo
demo/aheatmap.R
demo/00Index
demo/nmf.R demo/heatmaps.R
NEWS
data
data/esGolub.rda
R
R/extractFeatures.R R/Bioc-layer.R R/utils.R R/NMFStrategy-class.R R/atracks.R R/registry.R R/algorithms-brunet.R R/parallel.R R/seed-base.R R/versions.R R/NMFSet-class.R R/NMFOffset-class.R R/nmfModel.R R/registry-seed.R R/NMFstd-class.R R/NMFns-class.R R/aheatmap.R R/NMFStrategyIterative-class.R R/NMFplots.R R/data.R R/simulation.R R/seed-ica.R R/setNMFClass.R R/algorithms-base.R R/options.R R/NMF-class.R R/NMFStrategyFunction-class.R R/colorcode.R R/algorithms-lnmf.R R/run.R R/NMFSeed-class.R R/algorithms-snmf.R R/NMFStrategyOctave-class.R R/nmf.R R/registry-algorithms.R R/seed-nndsvd.R R/rmatrix.R R/algorithmic.R R/rnmf.R R/nmf-package.R R/grid.R R/fixed-terms.R R/transforms.R R/NMFfit-class.R R/algorithms-pe-nmf.R R/algorithms-siNMF.R R/algorithms-lsnmf.R R/heatmaps.R R/tests.R
vignettes
vignettes/heatmaps.Rnw
vignettes/NMF-unitTests.Rnw
vignettes/src
vignettes/src/bmc.R vignettes/consensus.pdf
vignettes/.install_extras
vignettes/NMF-vignette.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/smoothing.Rd man/offset-nmf.Rd man/txtProgressBar.Rd man/setNMFSeed.Rd man/silhouette.NMF.Rd man/cophcor.Rd man/consensus-commaNMFfitX1-method.Rd man/NMFfitX-class.Rd man/fit.Rd man/bioc.Rd man/NMF-package.Rd man/staticVar.Rd man/seed.Rd man/show-commaNMFStrategyIterative-method.Rd man/advanced.Rd man/nmf.Rd man/types.Rd man/setNMFMethod.Rd man/NMFList-class.Rd man/nmf.equal.Rd man/terms-internal.Rd man/lsNMF-nmf.Rd man/deviance.Rd man/offset-commaNMFOffset-method.Rd man/residuals.Rd man/NMFfitXn-class.Rd man/NMFstd-class.Rd man/checkErrors.Rd man/nmfWrapper.Rd man/nmfModel.Rd man/scores.Rd man/nsNMF-nmf.Rd man/show-commaNMFfitX-method.Rd man/show-commaNMFfitXn-method.Rd man/parse_formula.Rd man/algorithm-commaNMFList-method.Rd man/nmfApply.Rd man/ccBreaks.Rd man/show-commaNMFfit-method.Rd man/nmfObject.Rd man/profplot.Rd man/NMFSeed-class.Rd man/runtime.all-commaNMFfitXn-method.Rd man/nmfEstimateRank.Rd man/basiscor.Rd man/subset-NMF.Rd man/revPalette.Rd man/rss.Rd man/show-commaNMFOffset-method.Rd man/connectivity.Rd man/rmatrix.Rd man/parallel.Rd man/plot-commaNMFfit-commamissing-method.Rd man/Strategy-class.Rd man/ccPalette.Rd man/offset-commaNMFfit-method.Rd man/nmf_update_KL.Rd man/nmfCheck.Rd man/aheatmap.Rd man/utils.Rd man/rnmf.Rd man/assess.Rd man/cutdendro.Rd man/predict.Rd man/randomize.Rd man/algorithm-commaNMFStrategyOctave-method.Rd man/NMFStrategyIterative-class.Rd man/NMF-defunct.Rd man/nmf_update_euclidean.Rd man/options.Rd man/nneg.Rd man/ccSpec.Rd man/NMF-class.Rd man/SNMF-nmf.Rd man/cluster_mat.Rd man/NMFStrategy-class.Rd man/sparseness.Rd man/KL-nmf.Rd man/c-commaNMF-method.Rd man/basis-coef-methods.Rd man/NMFns-class.Rd man/NMF-deprecated.Rd man/consensus-commaNMFfitXn-method.Rd man/nmfFormals.Rd man/lverbose.Rd man/fcnnls.Rd man/NMFStrategyFunction-class.Rd man/purity.Rd man/nmf-compare.Rd man/NMFOffset-class.Rd man/heatmaps.Rd man/NMFStrategyOctave-class.Rd man/dims.Rd man/nmfReport.Rd man/stop-NMF.Rd man/inplace.Rd man/algorithmic.Rd man/runtime-commaNMFList-method.Rd man/show-commaNMFns-method.Rd man/scale.NMF.Rd man/atrack.Rd man/grid.Rd man/foreach.Rd man/fitted.Rd man/gfile.Rd man/canFit.Rd man/ccRamp.Rd man/terms.Rd man/dispersion.Rd man/consensushc.Rd man/match_atrack.Rd man/show-commaNMFfitX1-method.Rd man/dimnames.Rd man/registry-algorithm.Rd man/NMFfit-class.Rd man/show-commaNMFSeed-method.Rd man/setup.Rd man/show-commaNMF-method.Rd man/syntheticNMF.Rd man/nmfSeed.Rd man/objective-commaNMFfit-method.Rd man/show-commaNMFList-method.Rd man/NMFfitX.Rd man/dot-fcnnls.Rd man/NMFfitX1-class.Rd man/RNG.Rd man/NMFStrategy.Rd man/Frobenius-nmf.Rd man/esGolub.Rd man/t.NMF.Rd man/nmfAlgorithm.Rd
.Rinstignore
NMF documentation built on May 29, 2017, 9:40 a.m.