shbrief/GenomicSuperSignaturePaper
Reproduce GenomicSuperSignature paper

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Reproduce GenomicSuperSignature paper

.Rbuildignore
.gitignore
.nojekyll
DESCRIPTION
Methods/5_Hierarchical_Clustering_with_SpikeInTCGA_moreNegControl.Rmd Methods/select_numOfClusters/evaluateCluster.R Methods/select_numOfClusters/find_optimum_k.Rmd Methods/select_numOfClusters/neg_controls.R
Methods/select_numOfClusters/outputs/png/A.heatmap_neg50.png
Methods/select_numOfClusters/outputs/png/B.separatedPortion.png
Methods/select_numOfClusters/outputs/png/C.numUnseparated.png
Methods/select_numOfClusters/outputs/png/Sup_Fig_3.png
Methods/training_datasets/accessions.rds
Methods/training_datasets/available_samples.Rmd
NAMESPACE
PCAGenomicSignaturesPaper.Rproj
R/LVScatter.R R/checkPathwaySeparation.R R/commonGene.R R/misc.R README.md Results/CRC/CRC_ClinicalVar.Rmd Results/CRC/CRC_Subtyping.Rmd Results/CRC/Figures/README.md
Results/CRC/Figures/manuscript_Fig3.png
Results/CRC/Figures/manuscript_Fig3a.png
Results/CRC/Figures/manuscript_Fig3b.png
Results/CRC/Figures/manuscript_Fig3c.png
Results/CRC/Figures/manuscript_Sup_Fig5.png
Results/CRC/Figures/manuscript_Sup_Fig6.png
Results/CRC/Figures/rawData_1575_834_10valData.csv
Results/CRC/Figures/rawData_1575_834_18valData.csv
Results/CRC/Figures/rawData_832_188_10valData.csv
Results/CRC/Figures/rawData_832_188_18valData.csv
Results/CRC/Figures/rawData_834_833_10valData.csv
Results/CRC/Figures/rawData_834_833_18valData.csv
Results/CRC/Figures/rawData_PCSS1_PCSS2_10valData.csv
Results/CRC/Figures/rawData_PCSS1_PCSS2_18valData.csv
Results/CRC/PCSS_vs_RAV.Rmd Results/CRC/R/Fig4A_PCSS.R Results/CRC/R/Fig4A_plotting.R Results/CRC/R/Fig4C_CMSvs.R Results/CRC/R/Fig4C_contScores.R Results/CRC/R/Fig4_add_sampleScore.R Results/CRC/README.md
Results/CRC/data/SummaryForFig4.rds
Results/CRC/data/avg_loadings.csv
Results/CRC/data/eSets/datasetSummary.txt
Results/CRC/data/eSets/setNames.RData
Results/CRC/data/eSets/trainingSetNames.RData
Results/CRC/data/results/model_comparison/CMS/PCSS1_PCSS2_10_valData.csv
Results/CRC/data/results/model_comparison/CMS/PCSS1_PCSS2_18_valData.csv
Results/CRC/data/results/model_comparison/CMS/RAV1575_RAV834_18_valData.csv
Results/CRC/data/results/model_comparison/CMS/RAV832_RAV188_18_valData.csv
Results/CRC/data/results/model_comparison/CMS/RAV834_RAV833_10_valData.csv
Results/CRC/data/results/model_comparison/CMS/RAV834_RAV833_18_valData.csv
Results/CRC/manuscript_Figures.Rmd Results/CRC/metadata_based_search.Rmd
Results/CRC/outputs/10_CRC_datasets/boxplot_CMS_vs_834_833.rds
Results/CRC/outputs/10_CRC_datasets/boxplot_CMS_vs_PCSS.rds
Results/CRC/outputs/10_CRC_datasets/boxplot_PCSS_vs_834_833.rds
Results/CRC/outputs/10_CRC_datasets/scatter_1575_834.rds
Results/CRC/outputs/10_CRC_datasets/scatter_834_833.rds
Results/CRC/outputs/10_CRC_datasets/scatter_PCSS.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_CMS_vs_1575_834.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_CMS_vs_832_188.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_CMS_vs_834_833.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_CMS_vs_PCSS.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_PCSS_vs_1575_834.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_PCSS_vs_832_188.rds
Results/CRC/outputs/18_CRC_datasets/boxplot_PCSS_vs_834_833.rds
Results/CRC/outputs/CRC_top10_validated_ind.tsv
Results/CRC/outputs/README.md
Results/CRC/outputs/boxplot_CMS_vs_1575_834.rds
Results/CRC/outputs/boxplot_CMS_vs_832_188.rds
Results/CRC/outputs/boxplot_CMS_vs_834_833.rds
Results/CRC/outputs/boxplot_CMS_vs_PCSS.rds
Results/CRC/outputs/boxplot_PCSS_vs_1575_834.rds
Results/CRC/outputs/boxplot_PCSS_vs_832_188.rds
Results/CRC/outputs/boxplot_PCSS_vs_834_3290.rds
Results/CRC/outputs/boxplot_PCSS_vs_834_596.rds
Results/CRC/outputs/boxplot_PCSS_vs_834_833.rds
Results/CRC/outputs/boxplot_summary.csv
Results/CRC/outputs/png/boxplot_CMS_vs_832_188.png
Results/CRC/outputs/png/boxplot_CMS_vs_834_833.png
Results/CRC/outputs/png/boxplot_PCSS_vs_834_833.png
Results/CRC/outputs/png/scatter_834_833.png
Results/CRC/outputs/scatter_1575_834.rds
Results/CRC/outputs/scatter_832_188.rds
Results/CRC/outputs/scatter_834_833.rds
Results/CRC/outputs/scatter_PCSS.rds
Results/E-MTAB-2452/E-MTAB-2452.Rmd
Results/E-MTAB-2452/Figures/manuscript_Fig1B_bottomleft.png
Results/E-MTAB-2452/Figures/manuscript_Fig1B_bottomright.png
Results/E-MTAB-2452/Figures/manuscript_Fig1B_topleft.png
Results/E-MTAB-2452/Figures/manuscript_Sup_Fig8.png
Results/E-MTAB-2452/data/E-MTAB-2452_hugene11st_SCANfast_with_GeneSymbol.pcl
Results/NARES/data/NARES_ComBat_MCPCounter_results_tidy.tsv
Results/NARES/data/NARES_SCANfast_ComBat_with_GeneSymbol.pcl
Results/NARES/data/NARES_demographic_data.tsv
Results/NARES/neutrophil_counts_NARES.Rmd
Results/NARES/outputs/nares_neutrophil.rds
Results/NARES/outputs/png/nares_neutrophil.png
Results/README.md Results/SLE-WB/README.md Results/SLE-WB/neutrophil_counts_SLE-WB.Rmd
Results/SLE-WB/outputs/neutrophil_count.rds
Results/SLE-WB/outputs/png/neutrophil_count.png
Results/SLE-WB/outputs/png/neutrophil_estimate.png
Results/TCGA/Figures/manuscript_Fig2.png
Results/TCGA/Figures/manuscript_Fig2a.png
Results/TCGA/Figures/manuscript_Fig2b.png
Results/TCGA/Figures/manuscript_Fig2c.png
Results/TCGA/Figures/manuscript_Fig2d.png
Results/TCGA/Figures/manuscript_Fig2e.png
Results/TCGA/Figures/manuscript_Sup_Fig4.png
Results/TCGA/Figures/manuscript_Sup_Fig4C.png
Results/TCGA/R/build_TCGA_validationDatasets.R Results/TCGA/TCGA_5studies.Rmd Results/manuscript.Rmd Results/manuscript.pdf
Results/manuscript_files/figure-html/unnamed-chunk-3-1.png
Results/manuscript_files/figure-html/unnamed-chunk-3-2.png
Results/manuscript_files/figure-html/unnamed-chunk-3-3.png
Results/manuscript_files/figure-html/unnamed-chunk-3-4.png
Results/manuscript_files/figure-html/unnamed-chunk-4-1.png
Results/manuscript_files/figure-html/unnamed-chunk-4-2.png
Results/manuscript_files/figure-html/unnamed-chunk-4-3.png
Results/manuscript_files/figure-html/unnamed-chunk-4-4.png
Results/manuscript_files/figure-html/unnamed-chunk-4-5.png
Results/manuscript_files/figure-html/unnamed-chunk-4-6.png
Results/model/Characterize_GSEA.Rmd Results/model/LINC.R Results/model/LINC.Rmd Results/model/PC_selection.Rmd Results/model/PCs_In_Clusters.Rmd Results/model/PCs_In_Clusters.pdf
Results/model/RAVs_with_topPCs.tsv
Results/model/README.md Results/model/Simulate_PCSSs.Rmd Results/model/Top10PCs_RAVmodel.Rmd Results/model/What_RAVmodel_Is.Rmd Results/model/listOfRAVmodels.R
Results/model/lowerPCsInClusters.csv
Results/model/manuscript_SupFig11.png
Results/model/manuscript_SupFig9.png
Results/model/pathwayCoverage.R
Results/model/pcNumAll.tsv
Results/multiPLIER_Fig3.Rmd
Results/multiPLIER_Fig3.png
Results/others/available_samples.png
Results/others/repeat_Fig5_Pathway_Separation.Rmd Workshop/BioC2022_GSS_slide.pdf Workshop/BioC2022_GSS_vignette.Rmd Workshop/README.md
_pkgdown.yml
index.md inst/README.md
inst/extdata/MeSH_terms_1399refinebio.rda
inst/extdata/SupTable3_RAVmodels.csv
inst/extdata/source_name_annotated.tsv
inst/extdata/topGenes_13934.rds
inst/images/CRC_Fig4A.png
inst/images/CRC_Fig4C.png
inst/images/GSig_RAVmodel.png
inst/images/GSig_knowledge_graph.png
inst/images/multiPLIER_Fig3.png
inst/script/miniRAVmodel.R man/LVScatter.Rd man/checkPathwaySeparation.Rd man/commonGene.Rd man/getAssociatedRAVs.Rd man/gg_color_hue.Rd
update.sh
shbrief/GenomicSuperSignaturePaper documentation built on Aug. 2, 2022, 2:04 p.m.

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