Files in naikai/sake
Single-cell RNA-Seq Analysis and Klustering Evaluation
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/clanc.R
R/clanc_utils.R
R/corModule.R
R/cv_utils.R
R/data.R
R/data_utils.R
R/format_utils.R
R/heatmap.3.R
R/heatmap_utils.R
R/misc.R
R/multiplot.R
R/networkModule.R
R/network_utils.R
R/nmf_utils.R
R/nmfresModule.R
R/plot_utils.R
R/sake-package.r
R/test.R
R/tsne_utils.R
README.Rmd
README.md
data/Ting.NMF5.rda
data/Treutlein.NMF4.rda
data/Usoskin.rda
inst/extdata/genefile/breastClassifier_PAM50genes_forTCGA.txt
inst/extdata/genefile/genelist.Aviv.txt
inst/extdata/genefile/genelist.AvivMelanomaCellCycle.txt
inst/extdata/genefile/genelist.BRCA-NMF-K5.txt
inst/extdata/genefile/genelist.CellCycle.txt
inst/extdata/genefile/genelist.EMT.txt
inst/extdata/genefile/genelist.Hoek.txt
inst/extdata/genefile/genelist.KRAS.txt
inst/extdata/genefile/genelist.Melanoma-20miRNA.txt
inst/extdata/genefile/genelist.Mouse_CellCycle.txt
inst/extdata/genefile/genelist.Mouse_RegCellCycle.txt
inst/extdata/genefile/genelist.MyFourGroups.txt
inst/extdata/genefile/genelist.PAM50.txt
inst/extdata/genefile/genelist.PubResistList.txt
inst/extdata/genefile/genelist.PubResistList_core.txt
inst/extdata/genefile/genelist.RegCC.txt
inst/extdata/genefile/genelist.SKCM-NMF-K3-VST-1000nrun.txt
inst/extdata/genefile/genelist.SKCM-NMF-K3.txt
inst/extdata/genefile/genelist.SKCM-NMF-K3_tempsave.txt
inst/extdata/genefile/genelist.SKCM-NMF-K4.txt
inst/extdata/genefile/genelist.Stein.txt
inst/extdata/genefile/genelist.Stein_core.txt
inst/extdata/genefile/genelist.WNT.txt
inst/extdata/genefile/genelist.WNT_KRAS.txt
inst/extdata/genefile/genelist.Widmer.txt
inst/extdata/geneset/Homo_sapiens_GSEA_GO_sets_all_symbols_April_2015.gmt
inst/extdata/geneset/Homo_sapiens_GSEA_GO_sets_bp_symbols_April_2015.gmt
inst/extdata/geneset/Homo_sapiens_GSEA_GO_sets_cc_symbols_April_2015.gmt
inst/extdata/geneset/Homo_sapiens_GSEA_GO_sets_mf_symbols_April_2015.gmt
inst/extdata/geneset/c1.all.v5.0.symbols.gmt
inst/extdata/geneset/c2.all.v5.0.symbols.gmt
inst/extdata/geneset/c2.cgp.v5.0.symbols.gmt
inst/extdata/geneset/c2.cp.biocarta.v5.0.symbols.gmt
inst/extdata/geneset/c2.cp.kegg.v5.0.symbols.gmt
inst/extdata/geneset/c2.cp.reactome.v5.0.symbols.gmt
inst/extdata/geneset/c2.cp.v5.0.symbols.gmt
inst/extdata/geneset/c3.all.v5.0.symbols.gmt
inst/extdata/geneset/c3.mir.v5.0.symbols.gmt
inst/extdata/geneset/c3.tft.v5.0.symbols.gmt
inst/extdata/geneset/c4.all.v5.0.symbols.gmt
inst/extdata/geneset/c4.cgn.v5.0.symbols.gmt
inst/extdata/geneset/c4.cm.v5.0.symbols.gmt
inst/extdata/geneset/c5.all.symbols.highquality_April_2015.gmt
inst/extdata/geneset/c5.bp.symbols.highquality_April_2015.gmt
inst/extdata/geneset/c5.cc.symbols.highquality_April_2015.gmt
inst/extdata/geneset/c5.mf.symbols.highquality_April_2015.gmt
inst/extdata/geneset/c6.all.v5.0.symbols.gmt
inst/extdata/geneset/c7.all.v5.0.symbols.gmt
inst/extdata/geneset/h.all.v5.0.symbols.gmt
inst/extdata/rawdata/GSE51372_readCounts-paper.txt
inst/extdata/rawdata/GSE67310_iN_d0d2_expinfo.txt
inst/extdata/rawdata/GSE67310_iN_d0d5_expinfo.txt
inst/extdata/rawdata/GSE67310_iN_d20d22_expinfo.txt
inst/sake/.gitignore
inst/sake/global.R
inst/sake/server.r
inst/sake/ui.R
inst/sake/www/google-analytics.js
man/NetConnectivity.Rd
man/Usoskin.Rd
man/affy_probe_to_gene_symbol.Rd
man/assign_label_cex.Rd
man/cal_entropy.Rd
man/centroid_classify.Rd
man/clean_iterNMF.Rd
man/clust_by_hier.Rd
man/clust_silhouette.Rd
man/comp_module_genelist.Rd
man/compare_group.Rd
man/compare_groups_stats.Rd
man/connect_gap_modules.Rd
man/corModuleUI.Rd
man/cor_mtest.Rd
man/create.brewer.color.Rd
man/create.manual.color.Rd
man/create_centroid.Rd
man/def_net_module2.Rd
man/def_net_modules.Rd
man/deseq_norm.Rd
man/detect_genecnt_platform.Rd
man/ext_gene_function.Rd
man/extract_data_by_mad.Rd
man/extract_data_by_math.Rd
man/gene_convert_human_to_mouse.Rd
man/gene_convert_mouse_to_human.Rd
man/get_ClaNC_group.Rd
man/getcentroid.Rd
man/heatmap.3.Rd
man/hello.Rd
man/is.whole.Rd
man/iter_nmf.Rd
man/load_genelist.Rd
man/load_geneset.Rd
man/module_finder.Rd
man/multiplot.Rd
man/mutual_info_from_confmatrix.Rd
man/mutual_info_from_vector.Rd
man/my.write.matrix.Rd
man/myHeatmap.3.Rd
man/myNMF.Rd
man/myboxplot.Rd
man/myd3Heatmap.Rd
man/myfread.table.Rd
man/name_to_color.Rd
man/nmf_estim_plot.Rd
man/nmf_extract_feature.Rd
man/nmf_extract_group.Rd
man/nmf_plot.Rd
man/nmf_select_best_k.Rd
man/nmf_silhouette_plot.Rd
man/nmf_summary.Rd
man/norm_factors.Rd
man/parse_tsne_res.Rd
man/pcaplot.Rd
man/plot_gene_expression.Rd
man/plot_modules.Rd
man/plot_tsne.Rd
man/predict_from_centroid.Rd
man/preprocessNetCon.Rd
man/reorderfun.Rd
man/rmv_constant_0.Rd
man/run_CV.Rd
man/run_ClaNC.Rd
man/run_CoExpression.Rd
man/run_DESeq2.Rd
man/run_icash.Rd
man/run_tsne.Rd
man/sake.Rd
man/scale_data.Rd
man/screenshot_plotly.Rd
man/select_n_pct.Rd
man/select_top_n.Rd
man/simpleCap.Rd
man/summarize_module2.Rd
man/top_genes.Rd
man/vst.Rd
man/weighted.silhouette.Rd
man/wgcna_ext_hubgenes.Rd
sake.Rproj
testfile
tests/testthat/testthat.R
vignettes/DE_Enrich.Rmd
vignettes/DE_Enrich.html
vignettes/DE_Enrich.md
vignettes/Data_Input.Rmd
vignettes/Data_Input.html
vignettes/Data_Input.md
vignettes/Figures/SAKE_workflow.png
vignettes/Figures/Ting/Estim.png
vignettes/Figures/Ting/Gene_network.png
vignettes/Figures/Ting/NMF_Ting_EstimK_consensus.png
vignettes/Figures/Ting/NMF_Ting_EstimK_stats.png
vignettes/Figures/Ting/NMF_Ting_K5_DESeq2_Group1.png
vignettes/Figures/Ting/NMF_Ting_K5_DESeq2_Group3.png
vignettes/Figures/Ting/NMF_Ting_K5_Enrich_Res.png
vignettes/Figures/Ting/NMF_Ting_K5_Enrich_Sel_Mouse.png
vignettes/Figures/Ting/NMF_Ting_K5_Feature.png
vignettes/Figures/Ting/NMF_Ting_K5_Group.png
vignettes/Figures/Ting/NMF_Ting_K5_PCA.png
vignettes/Figures/Ting/NMF_Ting_K5_PCA_Filename.png
vignettes/Figures/Ting/NMF_Ting_K5_PCA_Igfbp5.png
vignettes/Figures/Ting/NMF_Ting_K5_PCA_Klf4.png
vignettes/Figures/Ting/NMF_Ting_K5_Pathview.png
vignettes/Figures/Ting/NMF_Ting_K5_groupstats.png
vignettes/Figures/Ting/NMF_Ting_K5_heatmap.png
vignettes/Figures/Ting/NMF_Ting_K5_t-SNE.png
vignettes/Figures/Ting/Normalization.png
vignettes/Figures/Ting/QC_plot.png
vignettes/Figures/Ting/Sample_Correlation.png
vignettes/Figures/Ting/Scatter_plot.png
vignettes/Figures/Ting/SelTopMAD1500.png
vignettes/Figures/Ting/Transformation.png
vignettes/Figures/Ting/loaded_file.png
vignettes/Figures/Ting/logRPM.png
vignettes/Figures/Ting/preload.png
vignettes/Figures/Treutlein/Gene_network.png
vignettes/Figures/Treutlein/NMF_Treutlein_EstimK_consensus.png
vignettes/Figures/Treutlein/NMF_Treutlein_EstimK_stats.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_Enrich_Res.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_Enrich_Sel_Mouse.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_Enrich_pathview.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_Feature.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_Group.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_NMF_res.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_PCA.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_groupstats.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_heatmap.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_t-SNE_Filename.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_t-SNE_NMF.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_t-SNE_Syp.png
vignettes/Figures/Treutlein/NMF_Treutlein_K5_t-SNE_Tnnc2.png
vignettes/Figures/Treutlein/Normalization.png
vignettes/Figures/Treutlein/QC_plot.png
vignettes/Figures/Treutlein/Sample_Correlation.png
vignettes/Figures/Treutlein/Scatter_plot.png
vignettes/Figures/Treutlein/loaded_file.png
vignettes/Figures/Treutlein/preload.png
vignettes/Genelist_Filtering.Rmd
vignettes/Genelist_Filtering.html
vignettes/Genelist_Filtering.md
vignettes/NMF.Rmd
vignettes/NMF.html
vignettes/NMF.md
vignettes/Quality_Control.Rmd
vignettes/Quality_Control.html
vignettes/Quality_Control.md
vignettes/Ting.Rmd
vignettes/Ting.html
vignettes/Ting.md
vignettes/Ting_pdf.Rmd
vignettes/Ting_pdf.pdf
vignettes/Treutlein.Rmd
vignettes/Treutlein.html
vignettes/Treutlein.md
vignettes/Treutlein_pdf.Rmd
vignettes/Treutlein_pdf.pdf
vignettes/Visualization.Rmd
vignettes/Visualization.html
vignettes/Visualization.md
