Files in BaderLab/netDx
Network-based patient classifier
.BBSoptions
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
NEWS
R/Nets_writeSIF.R
R/RR_featureTally.R
R/buildPredictor.R
R/buildPredictor_sparseGenetic.R
R/callFeatSel.R
R/cleanPathwayName.R
R/compareShortestPath.R
R/compileFeatureScores.R
R/compileFeatures.R
R/countPatientsInNet.R
R/createPSN_MultiData.R
R/dataList2list.R
R/enrichLabelNets.R
R/fileCache.R
R/getCorrType.R
R/getEmapInput.R
R/getEmapInput_many.R
R/getFeatureScores.R
R/getNetConsensus.R
R/getPatientPredictions.R
R/getPatientRankings.R
R/getRegionOL.R
R/getSimilarity.R
R/globals.R
R/helper.R
R/makePSN_NamedMatrix.R
R/makePSN_RangeSets.R
R/makeQueries.R
R/makeSymmetric.R
R/mapNamedRangesToSets.R
R/matrix_getIJ.R
R/moveInteractionNets.R
R/perfCalc.R
R/plotEmap.R
R/plotIntegratedPatientNetwork.R
R/plotPerf.R
R/plotPerf_multi.R
R/plotPerf_simple.R
R/predict.R
R/predictPatientLabels.R
R/pruneNetByStrongest.R
R/pruneNet_pctX.R
R/pruneNets.R
R/readPathways.R
R/runFeatureSelection.R
R/runProfileToNetworks.R
R/runQuery.R
R/setupFeatureDB.R
R/similarities.R
R/simpleCap.R
R/smooMutationPropagation.R
R/sparsenet_enrichment_functions.R
R/sparsify2.R
R/sparsify3.R
R/splitTestTrain_partition.R
R/splitTestTrain_resampling.R
R/updateNets.R
R/utils.R
R/writeQueryBatchFile.R
R/writeQueryFile.R
R/writeWeightedNets.R
R/zzz.R
README.md
data/MB.pheno.rda
data/cnv_GR.rda
data/cnv_TTstatus.rda
data/cnv_netPass.rda
data/cnv_netScores.rda
data/cnv_patientNetCount.rda
data/cnv_pheno.rda
data/confmat.rda
data/featScores.rda
data/genes.rda
data/modelres.rda
data/npheno.rda
data/pathwayList.rda
data/pathway_GR.rda
data/pheno.rda
data/pheno_full.rda
data/predRes.rda
data/silh.rda
data/toymodel.rda
data/xpr.rda
inst/CITATION
inst/extdata/AGP1_CNV.txt
inst/extdata/GM_NRANK/CV_1.query-results.report.txt.NRANK
inst/extdata/GM_NRANK/CV_2.query-results.report.txt.NRANK
inst/extdata/GM_PRANK/CV_1.query-results.report.txt.PRANK
inst/extdata/GM_PRANK/CV_2.query-results.report.txt.PRANK
inst/extdata/GM_query.txt
inst/extdata/INSTALL/Dockerfile
inst/extdata/INSTALL/INSTALL_OSX.sh
inst/extdata/INSTALL/INSTALL_Unix.sh
inst/extdata/TGCT_mutSmooth_geno.txt
inst/extdata/TGCT_mutSmooth_pheno.txt
inst/extdata/dbPath/1/_0.cfs
inst/extdata/dbPath/1/metadata.xml
inst/extdata/dbPath/1/segments.gen
inst/extdata/dbPath/1/segments_2
inst/extdata/dbPath/base/_0.cfs
inst/extdata/dbPath/base/segments.gen
inst/extdata/dbPath/base/segments_2
inst/extdata/dbPath/cache/CORE/1/1.ser
inst/extdata/dbPath/cache/CORE/1/2.ser
inst/extdata/dbPath/cache/CORE/1/3.ser
inst/extdata/dbPath/cache/CORE/1/4.ser
inst/extdata/dbPath/cache/CORE/1/DatasetInfo.ser
inst/extdata/dbPath/cache/CORE/1/attributeGroups.ser
inst/extdata/dbPath/cache/CORE/1/networkIds.ser
inst/extdata/dbPath/cache/CORE/1/nodeIds.ser
inst/extdata/dbPath/genemania.xml
inst/extdata/dbPath/user/segments.gen
inst/extdata/dbPath/user/segments_1
inst/extdata/example_nets/BIG_CASE.txt
inst/extdata/example_nets/BIG_CONTROL.txt
inst/extdata/example_nets/BOTH_EQUAL.txt
inst/extdata/example_nets/MOSTLY_CASE.txt
inst/extdata/example_nets/SMALL_CASE.txt
inst/extdata/example_nets/SMALL_CONTROL.txt
inst/extdata/example_output/inputNets.txt
inst/extdata/example_output/rng1/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/example_output/rng1/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng1/predictionResults.txt
inst/extdata/example_output/rng2/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/example_output/rng2/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng2/predictionResults.txt
inst/extdata/example_output/rng3/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/example_output/rng3/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng3/predictionResults.txt
inst/extdata/genemania.xml
inst/extdata/pathway_ex3.gmt
inst/extdata/pathways.gmt
inst/extdata/plots/SURVIVENO.gmt
inst/extdata/plots/SURVIVENO_nodeAttrs.txt
inst/extdata/plots/SURVIVEYES.gmt
inst/extdata/plots/SURVIVEYES_nodeAttrs.txt
man/MB.pheno.Rd
man/RR_featureTally.Rd
man/avgNormDiff.Rd
man/buildPredictor.Rd
man/buildPredictor_sparseGenetic.Rd
man/callFeatSel.Rd
man/callOverallSelectedFeatures.Rd
man/cleanPathwayName.Rd
man/cnv_GR.Rd
man/cnv_TTstatus.Rd
man/cnv_netPass.Rd
man/cnv_netScores.Rd
man/cnv_patientNetCount.Rd
man/cnv_pheno.Rd
man/compareShortestPath.Rd
man/compileFeatureScores.Rd
man/compileFeatures.Rd
man/confmat.Rd
man/confusionMatrix.Rd
man/convertProfileToNetworks.Rd
man/countIntType.Rd
man/countIntType_batch.Rd
man/countPatientsInNet.Rd
man/createPSN_MultiData.Rd
man/dataList2List.Rd
man/dot-get_cache.Rd
man/enrichLabelNets.Rd
man/featScores.Rd
man/fetchPathwayDefinitions.Rd
man/genes.Rd
man/getCorrType.Rd
man/getEMapInput.Rd
man/getEMapInput_many.Rd
man/getEnr.Rd
man/getFeatureScores.Rd
man/getFileSep.Rd
man/getGMjar_path.Rd
man/getNetConsensus.Rd
man/getOR.Rd
man/getPSN.Rd
man/getPatientPredictions.Rd
man/getPatientRankings.Rd
man/getPerformance.Rd
man/getRegionOL.Rd
man/getResults.Rd
man/getSimilarity.Rd
man/makeInputForEnrichmentMap.Rd
man/makePSN_NamedMatrix.Rd
man/makePSN_RangeSets.Rd
man/makeQueries.Rd
man/makeSymmetric.Rd
man/mapNamedRangesToSets.Rd
man/matrix_getIJ.Rd
man/modelres.Rd
man/moveInteractionNets.Rd
man/normDiff.Rd
man/npheno.Rd
man/pathwayList.Rd
man/pathway_GR.Rd
man/perfCalc.Rd
man/pheno.Rd
man/pheno_full.Rd
man/plotEmap.Rd
man/plotIntegratedPatientNetwork.Rd
man/plotPerf.Rd
man/plotPerf_multi.Rd
man/predRes.Rd
man/predict.Rd
man/predictPatientLabels.Rd
man/pruneNet.Rd
man/pruneNet_pctX.Rd
man/pruneNets.Rd
man/randAlphanumString.Rd
man/readPathways.Rd
man/replacePattern.Rd
man/runFeatureSelection.Rd
man/runQuery.Rd
man/setupFeatureDB.Rd
man/silh.Rd
man/sim.eucscale.Rd
man/sim.pearscale.Rd
man/simpleCap.Rd
man/smoothMutations_LabelProp.Rd
man/sparsify2.Rd
man/sparsify3.Rd
man/splitTestTrain.Rd
man/splitTestTrain_resampling.Rd
man/tSNEPlotter.Rd
man/thresholdSmoothedMutations.Rd
man/toymodel.Rd
man/updateNets.Rd
man/writeNetsSIF.Rd
man/writeQueryBatchFile.Rd
man/writeQueryFile.Rd
man/writeWeightedNets.Rd
man/xpr.Rd
tests/testthat.R
tests/testthat/test_buildpredictor.R
tests/testthat/test_suite.R
vignettes/BuildPredictor.Rmd
vignettes/EMap_realworld.png
vignettes/Emap_example_screenshot.png
vignettes/Predict_CaseControl_from_CNV.Rmd.old
vignettes/ThreeWayClassifier.Rmd
vignettes/ValidateNew.Rmd
vignettes/images/vignette1_design.jpg
vignettes/integratedPSN_MEAN_top0.10.png
vignettes/prepare_data.R
