Files in renozao/NMF
Algorithms and framework for Nonnegative Matrix Factorization (NMF)

.Rbuildignore
.Rinstignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/Bioc-layer.R R/NMF-class.R R/NMFOffset-class.R R/NMFSeed-class.R R/NMFSet-class.R R/NMFStrategy-class.R R/NMFStrategyFunction-class.R R/NMFStrategyIterative-class.R R/NMFStrategyOctave-class.R R/NMFfit-class.R R/NMFns-class.R R/NMFplots.R R/NMFstd-class.R R/aheatmap.R R/algorithmic.R R/algorithms-base.R R/algorithms-brunet.R R/algorithms-lnmf.R R/algorithms-lsnmf.R R/algorithms-pe-nmf.R R/algorithms-siNMF.R R/algorithms-snmf.R R/atracks.R R/colorcode.R R/data.R R/extractFeatures.R R/fixed-terms.R R/grid.R R/heatmaps.R R/nmf-package.R R/nmf.R R/nmfModel.R R/options.R R/parallel.R R/registry-algorithms.R R/registry-seed.R R/registry.R R/rmatrix.R R/rnmf.R R/run.R R/seed-base.R R/seed-ica.R R/seed-nndsvd.R R/setNMFClass.R R/simulation.R R/tests.R R/transforms.R R/utils.R R/versions.R README.md
TODO
data/esGolub.rda
demo/00Index
demo/aheatmap.R demo/heatmaps.R demo/lsNMF-nmf.R demo/nmf.R
inst/CITATION
inst/REFERENCES.bib
inst/doc/NMF-unitTests.pdf inst/doc/NMF-vignette.pdf inst/doc/aheatmaps.pdf inst/doc/heatmaps.pdf
inst/m-files/brunet-run.m
inst/m-files/brunet.R
inst/m-files/brunet.m
inst/scripts/grid.R inst/scripts/report.Rmd inst/tests/runit.NMFSet.r inst/tests/runit.NMFStrategy-class.r inst/tests/runit.NMFclass.r inst/tests/runit.NMFfit-class.r inst/tests/runit.aheatmap.R inst/tests/runit.algorithms.r inst/tests/runit.bioc.r inst/tests/runit.distance.r inst/tests/runit.interface.r inst/tests/runit.options.r inst/tests/runit.parallel.r inst/tests/runit.seed.r inst/tests/runit.utils.r man-roxygen/VirtualNMF.R man/Frobenius-nmf.Rd man/KL-nmf.Rd man/NMF-class.Rd man/NMF-defunct.Rd man/NMF-deprecated.Rd man/NMF-package.Rd man/NMFList-class.Rd man/NMFOffset-class.Rd man/NMFSeed-class.Rd man/NMFStrategy-class.Rd man/NMFStrategy.Rd man/NMFStrategyFunction-class.Rd man/NMFStrategyIterative-class.Rd man/NMFStrategyOctave-class.Rd man/NMFfit-class.Rd man/NMFfitX-class.Rd man/NMFfitX.Rd man/NMFfitX1-class.Rd man/NMFfitXn-class.Rd man/NMFns-class.Rd man/NMFstd-class.Rd man/RNG.Rd man/SNMF-nmf.Rd man/Strategy-class.Rd man/advanced.Rd man/aheatmap.Rd man/aheatmap_layout.Rd man/algorithm-commaNMFList-method.Rd man/algorithm-commaNMFStrategyOctave-method.Rd man/algorithmic.Rd man/assess.Rd man/atrack.Rd man/basis-coef-methods.Rd man/basiscor.Rd man/bioc.Rd man/c-commaNMF-method.Rd man/canFit.Rd man/ccBreaks.Rd man/ccPalette.Rd man/ccRamp.Rd man/ccSpec.Rd man/checkErrors.Rd man/cluster_mat.Rd man/connectivity.Rd man/consensus-commaNMFfitX1-method.Rd man/consensus-commaNMFfitXn-method.Rd man/consensushc.Rd man/cophcor.Rd man/cutdendro.Rd man/deviance.Rd man/dimnames.Rd man/dims.Rd man/dispersion.Rd man/dot-fcnnls.Rd man/esGolub.Rd man/fcnnls.Rd man/fit.Rd man/fitted.Rd man/foreach.Rd man/gfile.Rd man/grid.Rd man/heatmaps.Rd man/inplace.Rd man/lsNMF-nmf.Rd man/lverbose.Rd man/match_atrack.Rd man/nmf-compare.Rd man/nmf.Rd man/nmf.equal.Rd man/nmfAlgorithm.Rd man/nmfApply.Rd man/nmfCheck.Rd man/nmfEstimateRank.Rd man/nmfFormals.Rd man/nmfModel.Rd man/nmfObject.Rd man/nmfReport.Rd man/nmfSeed.Rd man/nmfWrapper.Rd man/nmf_update_KL.Rd man/nmf_update_euclidean.Rd man/nneg.Rd man/nsNMF-nmf.Rd man/objective-commaNMFfit-method.Rd man/offset-commaNMFOffset-method.Rd man/offset-commaNMFfit-method.Rd man/offset-nmf.Rd man/options.Rd man/parallel.Rd man/parse_formula.Rd man/plot-commaNMFfit-commamissing-method.Rd man/predict.Rd man/profplot.Rd man/purity.Rd man/randomize.Rd man/registry-algorithm.Rd man/residuals.Rd man/revPalette.Rd man/rmatrix.Rd man/rnmf.Rd man/rss.Rd man/runtime-commaNMFList-method.Rd man/runtime.all-commaNMFfitXn-method.Rd man/scale.NMF.Rd man/scores.Rd man/seed.Rd man/setNMFMethod.Rd man/setNMFSeed.Rd man/setup.Rd man/show-commaNMF-method.Rd man/show-commaNMFList-method.Rd man/show-commaNMFOffset-method.Rd man/show-commaNMFSeed-method.Rd man/show-commaNMFStrategyIterative-method.Rd man/show-commaNMFarray-method.Rd man/show-commaNMFfit-method.Rd man/show-commaNMFfitX-method.Rd man/show-commaNMFfitX1-method.Rd man/show-commaNMFfitXn-method.Rd man/show-commaNMFns-method.Rd man/silhouette.NMF.Rd man/smoothing.Rd man/sparseness.Rd man/staticVar.Rd man/stop-NMF.Rd man/subset-NMF.Rd man/syntheticNMF.Rd man/t.NMF.Rd man/terms-internal.Rd man/terms.Rd man/txtProgressBar.Rd man/types.Rd man/utils.Rd
src/distance.cpp
src/divergence.cpp
src/euclidean.cpp
src/utils.cpp
tests/doRUnit.R
vignettes/.install_extras
vignettes/NMF-unitTests.Rnw
vignettes/NMF-unitTests.tex
vignettes/NMF-vignette.Rnw
vignettes/NMF-vignette.tex
vignettes/Rpackages.bib
vignettes/aheatmaps.Rnw
vignettes/aheatmaps.tex
vignettes/cache/NMF-vignette/__packages
vignettes/cache/NMF-vignette/algo_default_ec3d1fc56022c572bb9659afd99d81fd.RData
vignettes/cache/NMF-vignette/algo_default_ec3d1fc56022c572bb9659afd99d81fd.rdb
vignettes/cache/NMF-vignette/algo_default_ec3d1fc56022c572bb9659afd99d81fd.rdx
vignettes/cache/NMF-vignette/algo_lee_9008c04ee05b0a52afdf13b8d79aeeca.RData
vignettes/cache/NMF-vignette/algo_lee_9008c04ee05b0a52afdf13b8d79aeeca.rdb
vignettes/cache/NMF-vignette/algo_lee_9008c04ee05b0a52afdf13b8d79aeeca.rdx
vignettes/cache/NMF-vignette/algo_multirun_c603c8bc327e7eb1e50f2068e3a0ec06.RData
vignettes/cache/NMF-vignette/algo_multirun_c603c8bc327e7eb1e50f2068e3a0ec06.rdb
vignettes/cache/NMF-vignette/algo_multirun_c603c8bc327e7eb1e50f2068e3a0ec06.rdx
vignettes/cache/NMF-vignette/algo_ns_ad0c25d8d15f6797ae9aed306270ce94.RData
vignettes/cache/NMF-vignette/algo_ns_ad0c25d8d15f6797ae9aed306270ce94.rdb
vignettes/cache/NMF-vignette/algo_ns_ad0c25d8d15f6797ae9aed306270ce94.rdx
vignettes/cache/NMF-vignette/algo_pe_6a0c65ce4b705403bdb8360f71fb4c79.RData
vignettes/cache/NMF-vignette/algo_pe_6a0c65ce4b705403bdb8360f71fb4c79.rdb
vignettes/cache/NMF-vignette/algo_pe_6a0c65ce4b705403bdb8360f71fb4c79.rdx
vignettes/cache/NMF-vignette/errorplot_compute_415ee97fee7e8c21218d003bb3357ab2.RData
vignettes/cache/NMF-vignette/errorplot_compute_415ee97fee7e8c21218d003bb3357ab2.rdb
vignettes/cache/NMF-vignette/errorplot_compute_415ee97fee7e8c21218d003bb3357ab2.rdx
vignettes/cache/NMF-vignette/estimate_rank_998db197a81e0a5e8488302618775921.RData
vignettes/cache/NMF-vignette/estimate_rank_998db197a81e0a5e8488302618775921.rdb
vignettes/cache/NMF-vignette/estimate_rank_998db197a81e0a5e8488302618775921.rdx
vignettes/cache/NMF-vignette/estimate_rank_random_bdc0589cad524bb91db30d5c42e66fc6.RData
vignettes/cache/NMF-vignette/estimate_rank_random_bdc0589cad524bb91db30d5c42e66fc6.rdb
vignettes/cache/NMF-vignette/estimate_rank_random_bdc0589cad524bb91db30d5c42e66fc6.rdx
vignettes/cache/NMF-vignette/force_seq_b98357aabeaf0b325deced1ac075f596.RData
vignettes/cache/NMF-vignette/force_seq_b98357aabeaf0b325deced1ac075f596.rdb
vignettes/cache/NMF-vignette/force_seq_b98357aabeaf0b325deced1ac075f596.rdx
vignettes/cache/NMF-vignette/multimethod_9a19977370f3e37a28ac17b1bc7121f5.RData
vignettes/cache/NMF-vignette/multimethod_9a19977370f3e37a28ac17b1bc7121f5.rdb
vignettes/cache/NMF-vignette/multimethod_9a19977370f3e37a28ac17b1bc7121f5.rdx
vignettes/cache/NMF-vignette/multirun_keep_7cd47c91b40494ae227e102de8b1df2f.RData
vignettes/cache/NMF-vignette/multirun_keep_7cd47c91b40494ae227e102de8b1df2f.rdb
vignettes/cache/NMF-vignette/multirun_keep_7cd47c91b40494ae227e102de8b1df2f.rdx
vignettes/cache/NMF-vignette/perftable_setup_edffda89b48b2536ae6e43b2ee73ea76.RData
vignettes/cache/NMF-vignette/perftable_setup_edffda89b48b2536ae6e43b2ee73ea76.rdb
vignettes/cache/NMF-vignette/perftable_setup_edffda89b48b2536ae6e43b2ee73ea76.rdx
vignettes/cache/NMF-vignette/seed_01b22cc7adada2da682677b2f166bb2f.RData
vignettes/cache/NMF-vignette/seed_01b22cc7adada2da682677b2f166bb2f.rdb
vignettes/cache/NMF-vignette/seed_01b22cc7adada2da682677b2f166bb2f.rdx
vignettes/cache/NMF-vignette/seed_numeric_81b43fba47db7557ecb6c5a3f3154f79.RData
vignettes/cache/NMF-vignette/seed_numeric_81b43fba47db7557ecb6c5a3f3154f79.rdb
vignettes/cache/NMF-vignette/seed_numeric_81b43fba47db7557ecb6c5a3f3154f79.rdx
vignettes/cache/heatmaps/__packages
vignettes/cache/heatmaps/estimate_8f49c4c1dafc103b8d713d4a643ac995.RData
vignettes/cache/heatmaps/estimate_8f49c4c1dafc103b8d713d4a643ac995.rdb
vignettes/cache/heatmaps/estimate_8f49c4c1dafc103b8d713d4a643ac995.rdx
vignettes/cache/heatmaps/fit_methods_558205b4f51662e93a42553bc95e6a1b.RData
vignettes/cache/heatmaps/fit_methods_558205b4f51662e93a42553bc95e6a1b.rdb
vignettes/cache/heatmaps/fit_methods_558205b4f51662e93a42553bc95e6a1b.rdx
vignettes/cache/heatmaps/model_cfce5e53cfb9d1d1f97512c38cd0459f.RData
vignettes/cache/heatmaps/model_cfce5e53cfb9d1d1f97512c38cd0459f.rdb
vignettes/cache/heatmaps/model_cfce5e53cfb9d1d1f97512c38cd0459f.rdx
vignettes/consensus.pdf vignettes/figure/NMF-vignette-errorplot1.pdf vignettes/figure/NMF-vignette-errorplot2.pdf vignettes/figure/NMF-vignette-estimate_rank_hm_include.pdf vignettes/figure/NMF-vignette-estimate_rank_plot.pdf vignettes/figure/NMF-vignette-estimate_rank_random.pdf vignettes/figure/NMF-vignette-heatmap_coef_basis_inc.pdf vignettes/figure/NMF-vignette-heatmap_consensus_inc.pdf vignettes/figure/NMF-vignette-heatmap_consensus_inc1.pdf vignettes/figure/NMF-vignette-heatmap_consensus_inc2.pdf vignettes/figure/aheatmaps-clustering.pdf vignettes/figure/aheatmaps-clustering1.pdf vignettes/figure/aheatmaps-clustering2.pdf vignettes/figure/aheatmaps-clustering3.pdf vignettes/figure/aheatmaps-dendrogram1.pdf vignettes/figure/aheatmaps-dendrogram2.pdf vignettes/figure/aheatmaps-dendrogram3.pdf vignettes/figure/aheatmaps-dendrogram4.pdf vignettes/figure/aheatmaps-dendrogram5.pdf vignettes/figure/aheatmaps-dendrogram6.pdf vignettes/figure/aheatmaps-dendrogram_custom.pdf vignettes/figure/aheatmaps-dendrogram_custom_plot.pdf vignettes/figure/aheatmaps-dendrogram_custom_plot1.pdf vignettes/figure/aheatmaps-dendrogram_custom_plot2.pdf vignettes/figure/aheatmaps-dendrogram_custom_plot3.pdf vignettes/figure/aheatmaps-dendrogram_custom_plot4.pdf vignettes/figure/aheatmaps-dendrogram_dendextend1.pdf vignettes/figure/aheatmaps-dendrogram_dendextend2.pdf vignettes/figure/aheatmaps-dendrogram_dendextend3.pdf vignettes/figure/aheatmaps-layout1.pdf vignettes/figure/aheatmaps-layout2.pdf vignettes/figure/aheatmaps-layout_scale.pdf vignettes/figure/aheatmaps-layout_scale1.pdf vignettes/figure/aheatmaps-layout_scale2.pdf vignettes/figure/aheatmaps-layout_scale3.pdf vignettes/figure/aheatmaps-layout_scale4.pdf vignettes/figure/heatmaps-basismap_res.pdf vignettes/figure/heatmaps-coefmap_custom.pdf vignettes/figure/heatmaps-coefmap_res.pdf vignettes/figure/heatmaps-consensusmap_estimate.pdf vignettes/figure/heatmaps-consensusmap_methods.pdf vignettes/figure/heatmaps-consensusmap_res.pdf vignettes/figure/heatmaps-heatmap_data.pdf
vignettes/heatmaps.Rnw
vignettes/heatmaps.tex
vignettes/src/bmc.R
renozao/NMF documentation built on Aug. 21, 2018, 3:42 a.m.