Files in bhklab/PanCuRx
Pancreatic Ductal Adenocarcinoma Tool-Kit
.Rbuildignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/class-ClinicalModel.R
R/class-CohortList.R
R/class-ConsensusMetaclusteringModel.R
R/class-CoxModel.R
R/class-GeneFuModel.R
R/class-ModelComparison.R
R/class-NCSModel.R
R/class-PCOSP.R
R/class-RGAModel.R
R/class-RLSModel.R
R/class-S4Model.R
R/class-SurvivalExperiment.R
R/class-SurvivalModel.R
R/classUnions.R
R/data.R
R/globals.R
R/methods-assignSubtypes.R
R/methods-barPlotModelComparison.R
R/methods-coerce.R
R/methods-compareModels.R
R/methods-densityPlotModelComparison.R
R/methods-dropNotCensored.R
R/methods-findCommonGenes.R
R/methods-findCommonSamples.R
R/methods-forestPlot.R
R/methods-getTopFeatures.R
R/methods-merge.R
R/methods-normalize.R
R/methods-plotNetworkGraph.R
R/methods-plotROC.R
R/methods-plotSurvivalCurves.R
R/methods-predictClasses.R
R/methods-rankFeatures.R
R/methods-runGSEA.R
R/methods-subset.R
R/methods-trainModel.R
R/methods-validateModel.R
R/utilities.R
data/CSPC_MAE.rda
data/cohortSubtypeDFs.rda
data/existingClassifierData.rda
data/sampleClinicalModel.rda
data/sampleCohortList.rda
data/sampleICGCmicro.rda
data/samplePCOSPmodel.rda
data/samplePCOSPpredList.rda
data/samplePCSIsurvExp.rda
data/sampleRGAmodel.rda
data/sampleRLSmodel.rda
data/sampleTrainedPCOSPmodel.rda
data/sampleValPCOSPmodel.rda
man/CSPC_MAE.Rd
man/ClinicalModel-class.Rd
man/ClinicalModel.Rd
man/CohortList-class.Rd
man/CohortList.Rd
man/ConsensusMetaclusteringModel-class.Rd
man/ConsensusMetaclusteringModel.Rd
man/CoxModel-class.Rd
man/CoxModel.Rd
man/GeneFuModel-class.Rd
man/GeneFuModel.Rd
man/ModelComparison-class.Rd
man/ModelComparison.Rd
man/NCSModel-class.Rd
man/NetworkCommunitySearchModel.Rd
man/PCOSP-class.Rd
man/PCOSP.Rd
man/PCOSP_or_ClinicalModel-class.Rd
man/PCOSP_or_RLS_or_RGA-class.Rd
man/RGAModel-class.Rd
man/RLSModel-class.Rd
man/RandomGeneAssignmentModel.Rd
man/RandomLabelShufflingModel.Rd
man/S4Model-class.Rd
man/SurvivalExperiment-class.Rd
man/SurvivalExperiment.Rd
man/SurvivalModel-class.Rd
man/SurvivalModel.Rd
man/assignColDataColumn.Rd
man/assignSubtypes-CohortList-list-method.Rd
man/assignSubtypes-SurvivalExperiment-data.frame-method.Rd
man/assignSubtypes.Rd
man/barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method.Rd
man/barPlotModelComparison.Rd
man/birnbaum.Rd
man/chen.Rd
man/cohortSubtypeDFs.Rd
man/compareModels-ModelComparison-SurvivalModel-method.Rd
man/compareModels-SurvivalModel-SurvivalModel-method.Rd
man/compareModels.Rd
man/densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-method.Rd
man/densityPlotModelComparison.Rd
man/dot-findAllCohortPairs.Rd
man/dot-randomSampleIndex.Rd
man/dropNotCensored-CohortList-method.Rd
man/dropNotCensored-SurvivalExperiment-method.Rd
man/dropNotCensored.Rd
man/existingClassifierData.Rd
man/findCommonGenes-CohortList-method.Rd
man/findCommonGenes-MultiAssayExperiment-method.Rd
man/findCommonGenes.Rd
man/findCommonSamples-CohortList-method.Rd
man/findCommonSamples.Rd
man/forestPlot-ModelComparison-method.Rd
man/forestPlot-PCOSP_or_ClinicalModel-method.Rd
man/forestPlot.Rd
man/getModelSeed-SurvivalModel-method.Rd
man/getModelSeed.Rd
man/getTopFeatures-MultiAssayExperiment-method.Rd
man/getTopFeatures-PCOSP-method.Rd
man/getTopFeatures-SummarizedExperiment-method.Rd
man/getTopFeatures.Rd
man/haiderSigScores.Rd
man/hasColDataColumns.Rd
man/merge-SurvivalExperiment-SurvivalExperiment-method.Rd
man/modelParams-S4Model-method.Rd
man/modelParams-set-S4Model-List_or_list_or_NULL-method.Rd
man/modelParams-set.Rd
man/modelParams.Rd
man/models-S4Model-method.Rd
man/models-SurvivalModel-method.Rd
man/models-set-S4Model-List_or_list_or_NULL-method.Rd
man/models-set-SurvivalModel-SimpleList-method.Rd
man/models-set.Rd
man/models.Rd
man/normalize-DFrame-method.Rd
man/normalize-MultiAssayExperiment-method.Rd
man/normalize-SummarizedExperiment-method.Rd
man/normalize-data.frame_or_matrix-method.Rd
man/normalsMAE.Rd
man/optimalKMinimizeAmbiguity.Rd
man/plotNetworkGraph-NCSModel-method.Rd
man/plotNetworkGraph.Rd
man/plotROC-PCOSP-method.Rd
man/plotROC.Rd
man/plotSurvivalCurves-CoxModel-method.Rd
man/plotSurvivalCurves.Rd
man/predictClasses-CohortList-ClinicalModel-method.Rd
man/predictClasses-CohortList-GeneFuModel-method.Rd
man/predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method.Rd
man/predictClasses-ConsensusMetaclusteringModel-ANY-method.Rd
man/predictClasses-NCSModel-ANY-method.Rd
man/predictClasses-SurvivalExperiment-ClinicalModel-method.Rd
man/predictClasses-SurvivalExperiment-GeneFuModel-method.Rd
man/predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method.Rd
man/predictClasses.Rd
man/preprocessCaret.Rd
man/rankFeatures-MultiAssayExperiment-method.Rd
man/rankFeatures-SummarizedExperiment-method.Rd
man/rankFeatures.Rd
man/removeColDataFactorColumns.Rd
man/removeFactorColumns.Rd
man/renameColDataColumns.Rd
man/renameColumns.Rd
man/runGSEA-PCOSP-data.frame-method.Rd
man/runGSEA.Rd
man/sampleClinicalModel.Rd
man/sampleCohortList.Rd
man/sampleICGCmicro.Rd
man/samplePCOSPmodel.Rd
man/samplePCOSPpredList.Rd
man/samplePCSIsurvExp.Rd
man/sampleRGAmodel.Rd
man/sampleRLSmodel.Rd
man/sampleTrainedPCOSPmodel.Rd
man/sampleValPCOSPmodel.Rd
man/show-S4Model-method.Rd
man/subset-CohortList-method.Rd
man/trainData-S4Model-method.Rd
man/trainData-set-S4Model-method.Rd
man/trainData-set.Rd
man/trainData.Rd
man/trainModel-ClinicalModel-method.Rd
man/trainModel-ConsensusMetaclusteringModel-method.Rd
man/trainModel-CoxModel-method.Rd
man/trainModel-GeneFuModel-method.Rd
man/trainModel-NCSModel-method.Rd
man/trainModel-PCOSP-method.Rd
man/trainModel-RGAModel-method.Rd
man/trainModel-RLSModel-method.Rd
man/trainModel.Rd
man/validateModel-ClinicalModel-CohortList-method.Rd
man/validateModel-ClinicalModel-SurvivalExperiment-method.Rd
man/validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method.Rd
man/validateModel-GeneFuModel-CohortList-method.Rd
man/validateModel-GeneFuModel-SurvivalExperiment-method.Rd
man/validateModel-PCOSP_or_RLS_or_RGA-CohortList-method.Rd
man/validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method.Rd
man/validateModel.Rd
man/validationData-S4Model-method.Rd
man/validationData-SurvivalModel-method.Rd
man/validationData-set-S4Model-List_or_list_or_NULL-method.Rd
man/validationData-set-SurvivalModel-CohortList-method.Rd
man/validationData-set.Rd
man/validationData.Rd
man/validationStats-S4Model-method.Rd
man/validationStats-SurvivalModel-method.Rd
man/validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method.Rd
man/validationStats-set-SurvivalModel-data.frame-method.Rd
man/validationStats-set.Rd
man/validationStats.Rd
tests/testthat.R
tests/testthat/test-ClinicalModel-constructor.R
tests/testthat/test-ClinicalModel-trainModel-predictClasses-validateModel.R
tests/testthat/test-GeneFuModel-constructor.R
tests/testthat/test-GeneFuModel-trainModel-predictClasses-validateModel.R
tests/testthat/test-ModelComparions-constructor.R
tests/testthat/test-PCOSP-constructor.R
tests/testthat/test-PCOSP-trainModel-predictClasses-validateModel.R
tests/testthat/test-RGAModel-constructor.R
tests/testthat/test-RLSModel-constructor.R
tests/testthat/test-SurvivalExperiment-coercion.R
tests/testthat/test-SurvivalExperiment-constructor.R
tests/testthat/test-SurvivalModel-accessors.R
tests/testthat/test-SurvivalModel-constructor.R
vignettes/CSPC_model_analysis.rmd
vignettes/PCOSP_model_analysis.Rmd
vignettes/PDATK_introduction.rmd
