Files in compbiomed/TBSignatureProfiler

Profile RNA-Seq Data Using TB Pathway Signatures

CODE_OF_CONDUCT.md LICENSE.md NEWS.md R/OriginalModel.R R/TBSPapp.R R/addTBsignature.R R/bootstrap.R R/data.R R/evaluate.R R/plot.R R/profile.R README.md index.md inst/shiny/app.R inst/shiny/server/server_auc.R inst/shiny/server/server_profiler.R inst/shiny/server/server_upload.R inst/shiny/server/server_visualization.R inst/shiny/ui/ui_auc.R inst/shiny/ui/ui_profiler.R inst/shiny/ui/ui_upload.R inst/shiny/ui/ui_visualization.R man/Bootstrap_LOOCV_LR_AUC.Rd man/COVIDsignatures.Rd man/LOOAUC_simple_multiple_noplot_one_df.Rd man/ObtainSampleScore_OriginalModel.Rd man/OriginalTrainingData.Rd man/SignatureQuantitative.Rd man/SulimanOriginalModel.Rd man/TBSPapp.Rd man/TB_hiv.Rd man/TB_indian.Rd man/TBcommon.Rd man/TBsignatures.Rd man/TBsignaturesSplit.Rd man/addTBsignature.Rd man/bootstrapAUC.Rd man/common_sigAnnotData.Rd man/compareAlgs.Rd man/compareBoxplots.Rd man/cv_glmnet_OriginalModel.Rd man/deseq2_norm_rle.Rd man/distinctColors.Rd man/dot-OriginalModel_NoRetraining.Rd man/dot-OriginalModel_Retraining.Rd man/evaluateOriginalModel.Rd man/knn_OriginalModel.Rd man/lda_OriginalModel.Rd man/mkAssay.Rd man/plotQuantitative.Rd man/randomForest_OriginalModel.Rd man/ref_combat_impute.Rd man/runTBsigProfiler.Rd man/sigAnnotData.Rd man/signatureBoxplot.Rd man/signatureGeneHeatmap.Rd man/signatureHeatmap.Rd man/signatureROCplot.Rd man/signatureROCplot_CI.Rd man/subsetGeneSet.Rd man/svm_OriginalModel.Rd man/tableAUC.Rd tests/packagecoverage.R tests/spelling.R tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-OriginalModel.R tests/testthat/test-addTBsignature.R tests/testthat/test-bootstrap.R tests/testthat/test-evaluate.R tests/testthat/test-plot.R tests/testthat/test-profile.R vignettes/rmd/OriginalModelTutorial.Rmd vignettes/rmd/SignatureAddition.Rmd vignettes/rmd/TBSig_Vignette.Rmd vignettes/rmd/shinytutorial.Rmd vignettes/tbspVignette.Rmd