├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── BICboxplot.R ├── Comp_labels.R ├── Definition_SignExp_object.R ├── EstimateParameters.R ├── Optimal_sigs.R ├── RcppExports.R ├── SignExp_learning.R ├── SignExp_plots.R ├── SignExp_tests.R ├── cpp_eBayesNMF.R ├── flow_aboutpage.R ├── flow_app.R ├── flow_clusteringmodule.R ├── flow_covariatemodule.R ├── flow_denovomodule.R ├── flow_documentation.R ├── flow_explorepage.R ├── flow_fittingmodule.R ├── flow_format.R ├── flow_tcgaexplorermodule.R ├── flow_validate.R ├── genMatrix.R ├── read.snv.context.R ├── signeR.R ├── sysdata.rda └── zzz.R ├── README.md ├── data ├── cosmic_data.rda ├── tcga_similarities.rda └── tcga_tumors.rda ├── inst ├── CITATION ├── extdata │ ├── 21_breast_cancers.mutations.txt │ ├── 21_breast_cancers.opportunity.txt │ ├── Cosmic_signatures_BRC.txt │ ├── clinical-test-signerflow.tsv │ ├── example.bed │ ├── example.maf │ ├── example.vcf │ ├── genome_help.md │ ├── iterations.md │ ├── knownsigs_help.md │ ├── metadata_help.md │ ├── opp_help.md │ ├── snv_help.md │ └── tcga_analysis.md └── www │ ├── about.md │ ├── assets │ ├── boxplot.ico │ ├── correlation.ico │ ├── cox.ico │ ├── km.ico │ ├── linear-regression.ico │ ├── sample-classification.ico │ ├── signer.png │ ├── signeranalysis.jpg │ └── tcgaexplorer.jpg │ ├── bootstrapTable.min.css │ ├── custom.css │ ├── footer.css │ └── footer.html ├── man ├── Diffexp.Rd ├── ExposureClassify.Rd ├── ExposureClassifyCV.Rd ├── ExposureCorrelation.Rd ├── ExposureFuzzyClustering.Rd ├── ExposureGLM.Rd ├── ExposureHierarchicalClustering.Rd ├── ExposureSurvModel.Rd ├── ExposureSurvival.Rd ├── cosmic_data.Rd ├── genMatrix.Rd ├── methods.Rd ├── plots.Rd ├── signeR-package.Rd ├── signeR.Rd ├── signeRFlow.Rd ├── signexp-class.Rd ├── tcga_similarities.Rd └── tcga_tumors.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── fuzzy.cpp ├── gibbs_2.cpp └── signeR_init.c └── vignettes ├── Model_selection_BICs.png ├── flow_clinical.png ├── flow_clinical_summary.png ├── flow_clustering_dist.png ├── flow_clustering_method.png ├── flow_cor.png ├── flow_cox.png ├── flow_de.png ├── flow_de_novo.png ├── flow_fitting.png ├── flow_fuzzy.png ├── flow_lr.png ├── flow_opp_upload.png ├── flow_overview.png ├── flow_previous_sig.png ├── flow_sc.png ├── flow_snv_upload.png ├── flow_sv.png ├── flow_tcga_data_summary.png ├── flow_tcga_explorer.png ├── flow_tcga_filter.png ├── flow_tcga_filter_covariate.png ├── signeR-vignette.Rhtml └── signeRFlow.Rmd /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TojalLab/signeR/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TojalLab/signeR/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: 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