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/RPM.Rd man/UQ.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/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_ID.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/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
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
naikai/sake documentation built on April 13, 2018, 8:44 p.m.