Files in ChristofferFlensburg/superFreq
Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.
DESCRIPTION
LICENSE
NAMESPACE
R/CNVnormalisation.R
R/XRank.R
R/addBindingStrength.R
R/analyse.R
R/bamToPileup.R
R/callCNVs.R
R/cohortAnalyseBatch.R
R/debug.R
R/downloadSuperFreqResources.R
R/generateHTML.R
R/genesOfInterest.R
R/get104signature.R
R/getStories.R
R/getVariantsByIndividual.R
R/importCaptureRegions.R
R/importSampleMetaData.R
R/makeCNVplots.R
R/makeFitPlots.R
R/makeRiverPlots.R
R/makeSNPprogressionPlots.R
R/makeScatterPlots.R
R/makeSummaryPlot.R
R/matchFlagVariants.R
R/meanCNV.R
R/mergeMethods.R
R/metaData.R
R/outputData.R
R/outputNewVariants.R
R/outputSomaticVariants.R
R/preliminaryVariantCalling.R
R/runDEexon.R
R/runVEP.R
R/runVariantAnnotation.R
README.md
data/entrez2symbol_hs.rda
data/entrez2symbol_mm.rda
man/VAconsequenceToSeverityRank.Rd
man/VAseverityToConsequence.Rd
man/addBindingStrength.Rd
man/analyse.Rd
man/annotateQ.Rd
man/annotateSomaticQs.Rd
man/bamToPileup.Rd
man/chrLengths.Rd
man/chrToX.Rd
man/cohortAnalyseBatch.Rd
man/cohortAnalyseBatchContrast.Rd
man/compareGroups.Rd
man/defaultSuperParameters.Rd
man/defaultSuperRuntimeSettings.Rd
man/defaultSuperSettings.Rd
man/downloadTemplate.Rd
man/dumpInput.Rd
man/forceRedoEverything.Rd
man/forceRedoNothing.Rd
man/get104profile.Rd
man/getCohortMutationMatrix.Rd
man/getCosmicCounts.Rd
man/getMoreVEPinfo.Rd
man/getSettings.Rd
man/getStories.Rd
man/getVariantsByIndividual.Rd
man/importCaptureRegions.Rd
man/importSampleMetaData.Rd
man/loadData.Rd
man/makeFitPlots.Rd
man/makeHeatmap.Rd
man/makepHeatmap.Rd
man/mcri.Rd
man/mergeBatches.Rd
man/moreVEPnames.Rd
man/plotCNAheatmapOverGoI.Rd
man/plotCNAheatmapWithGoI.Rd
man/plotCR.Rd
man/plotCohortMutationHeatmap.Rd
man/plotColourScatter.Rd
man/plotMA.Rd
man/plotRiver.Rd
man/plotStories.Rd
man/postAnalyseVEP.Rd
man/printHTML.Rd
man/qToGRanges.Rd
man/qualityScatter.Rd
man/requireFileExists.Rd
man/runDE.Rd
man/runSummaryPostAnalysis.Rd
man/runVEP.Rd
man/severityToType.Rd
man/superCohort.Rd
man/superFreq.Rd
man/superInputFiles.Rd
man/superOutputDirectories.Rd
man/superVersion.Rd
man/typeToSeverity.Rd
man/vafScatter.Rd
man/writeToVCF.Rd
man/xToChr.Rd
man/xToGene.Rd
man/xToPos.Rd
manual/manual.pdf
r-superfreq/bld.bat
r-superfreq/build.sh
r-superfreq/meta.yaml
readmeImages/TCGA.A3.3320.PrimaryTumor.WXS.fc2.png
readmeImages/all.png
readmeImages/multisample.png
readmeImages/river.png
superFreq.Rproj
