Files in sgosline/mpnstXenoModeling

MPNST Xenograft Modeling

R/bagOfGenesEnrichment.R R/data.R R/drugBiomarkers.R R/incucyteMetrics.R R/mtResponseMetrics.R R/plotDataSets.R R/synapseUtil.R R/xenoResponseMetrics.R R/xevaProcessing.R README.md bin/storeMutationalFilesInTable.R cellLineTreatment/pullFileAnnotations.R exp7_proteomicsAnalysis.Rmd exp8_proteomicsNetworks.Rmd loadPackages.R man/TryFit.Rd man/compress_enrichment.Rd man/computeAUC.Rd man/computeGRI.Rd man/computeTGI.Rd man/dataFromSynTable.Rd man/deseq2NormFilter.Rd man/doGSEA.Rd man/doRegularGo.Rd man/do_deseq_import.Rd man/drcmod.Rd man/drugMutationsCor.Rd man/drugTranscriptCor.Rd man/ds2FactorDE.Rd man/fixDrugData.Rd man/formatDataToXeva.Rd man/geneIdToSymbolMatrix.Rd man/generate_DR_plots.Rd man/generate_TR_plots.Rd man/getAllDrugStats.Rd man/getMicroTissueDrugData.Rd man/getNewSomaticCalls.Rd man/hypothesisTestPlotsDE.Rd man/limmaTwoFactorDEAnalysis.Rd man/loadIncucyteData.Rd man/loadMicrotissueDrugData.Rd man/loadMicrotissueMetadata.Rd man/loadPDXData.Rd man/loadPDXDrugData.Rd man/loadRNASeqData.Rd man/loadVariantData.Rd man/normDiffEx.Rd man/parseSynidListColumn.Rd man/plotCorrelationEnrichment.Rd man/plotDrugData.Rd man/plotGenesetResults.Rd man/plotIncTreatmentByDrug.Rd man/plotMTTreatmentByDrug.Rd man/plotMTTreatmentBySample.Rd man/plotPDXTreatmentBySample.Rd man/plotTopGenesHeatmap.Rd man/plotTumorGrowthCorrelations.Rd man/process_IncucyteDrugData.Rd man/queryPartSynapseTable.Rd man/querySynapseTable.Rd man/reverselog_trans.Rd man/statsForDrugPatient.Rd man/synTableStore.Rd man/synapseLogin.Rd man/synapseStore.Rd man/tidiedTableToExpressionSet.Rd results/GEM_tumorDeconvAnalysis.Rmd results/exp1_somaticVariantExpression.Rmd results/exp2_drugSensExpressionCorrelations.Rmd results/exp3_PDXdrugSensExpressionCorrelations.Rmd results/exp5_DoseResponsePlots.Rmd results/geneExpressionAnalysis.Rmd results/old_tests/01-molecular-drug-sig.Rmd results/old_tests/03-DEanalysis.Rmd results/old_tests/03-Gene-Network-Sig-Detection.Rmd results/old_tests/04-mutation-diversity.Rmd results/old_tests/06-testDrugNorm.Rmd results/old_tests/DEtest.Rmd results/old_tests/debugXeva.Rmd results/old_tests/doseResponsePlots.pdf results/old_tests/exp4_IncucyteDrugSensExpCor.Rmd results/old_tests/exp6_drugSynergyAnalysis.Rmd results/old_tests/fixIds.R results/old_tests/old-mut-cor.Rmd results/old_tests/runMultiPlier.R results/old_tests/ttest_MPNST.R results/shp2RnaSeq.Rmd results/summary_stats/calculateIncucyteDoseResponse.Rmd results/summary_stats/calculateMTDoseResponse.Rmd results/summary_stats/calculatePDXDoseResponse.Rmd results/tumorDeconvAnalysis.Rmd