Files in PNNL-CompBio/amlresistancenetworks
Calculates networks that lead to AML resistance to drugs
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
NAMESPACE
R/bagOfGenesEnrichment.R
R/data.R
R/dataManagement.R
R/drugSensitivityStats.R
R/molecularSigs.R
R/proteinNetworks.R
R/proteinValues.R
R/synapseUtil.R
R/trainAndTestMolSigs.R
README.md
amlresistancenetworks.Rproj
bin/06_networkTest.R
bin/amlPatientNetworks.py
bin/cellLineNetworks.py
bin/kinSubstrateNetwork.R
bin/runOnceCommands.R
bin/testMarkdowns/doGilteritinibNetworks.Rmd
bin/testMarkdowns/earlyVsLateAnalysis.Rmd
bin/testMarkdowns/runGilteritinibAnalysis.Rmd
data/testData.rda
inst/Kinase_Substrate_Dataset
inst/PSP&NetworKIN_Kinase_Substrate_Dataset_July2016.csv
inst/gene_attribute_edges.txt
man/buildFeatureMatrix.Rd
man/clusterDrugFamilyEfficacy.Rd
man/clusterSingleDrugEfficacy.Rd
man/computeAUCCorVals.Rd
man/computeDiffExByDrug.Rd
man/computeFoldChangePvals.Rd
man/computeGSEA.Rd
man/computeKSEA.Rd
man/computePhosphoChanges.Rd
man/computePhosphoNetwork.Rd
man/computeProteinNetwork.Rd
man/doRegularGo.Rd
man/doRegularKin.Rd
man/drugMolLogReg.Rd
man/drugMolLogRegEval.Rd
man/drugMolRandomForest.Rd
man/drugMolRegression.Rd
man/drugMolRegressionEval.Rd
man/findCandidates.Rd
man/getCoClusteredProteins.Rd
man/getCorrelatedProteins.Rd
man/getCytokineSensData.Rd
man/getFeaturesFromString.Rd
man/getFeaturesFromStringdf.Rd
man/getTimeCourseData.Rd
man/limmaTwoFactorDEAnalysis.Rd
man/manualDEAnalysis.Rd
man/mapPhosphoToKinase.Rd
man/miniForest.Rd
man/miniForestEval.Rd
man/miniLogR.Rd
man/miniLogREval.Rd
man/miniReg.Rd
man/miniRegEval.Rd
man/plotAllAUCs.Rd
man/plotCorrelationEnrichment.Rd
man/plotCorrelationsByDrug.Rd
man/plotGSEA.Rd
man/plotKinDat.Rd
man/plotOldGSEA.Rd
man/plotProtsByMetric.Rd
man/plotSingleProtein.Rd
man/querySynapseTable.Rd
man/readAndTidyMetadata.Rd
man/readAndTidyPhosphoProtMeasures.Rd
man/readAndTidyProtMeasures.Rd
man/readAndTidyQuizMetadata.Rd
man/readAndTidyQuizPhosphoProtMeasures.Rd
man/readAndTidyQuizProtMeasures.Rd
man/readAndTidySensMetadata.Rd
man/readAndTidySensPhosMeasures.Rd
man/readAndTidySensProtMeasure.Rd
man/readAndTidyUncorrectedQuizPhosphoMeasures.Rd
man/reverselog_trans.Rd
man/synTableStore.Rd
man/synTableUpdate.Rd
man/synapseLogin.Rd
man/synapseStore.Rd
man/testData.Rd
networkin.tsv.xz
results/singleComboResistance/03_giltDrugSensitivity.R
results/singleComboResistance/04_resistanceVsSensCombinations.R
results/singleComboResistance/07_phosphoSensAnalysis.R
tests/testthat.R
tests/testthat/test-testReg.R
