API for ChristofferFlensburg/superFreq
Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.
| Global functions | |
|---|---|
| CNVregionsPerBP | Source code |
| D3colour | Source code |
| D3colours | Source code |
| DEposterior | Source code |
| GLFC | Source code |
| GR | Source code |
| QCsnp | Source code |
| QCsnps | Source code |
| SNP2GRanges | Source code |
| VAconsequenceToSeverityRank | Man page Source code |
| VAseverityToConsequence | Man page Source code |
| XRank | Source code |
| addAnnotationToOutput | Source code |
| addBindingStrength | Man page Source code |
| addCCGDannotation | Source code |
| addCNAs | Source code |
| addCOSMICannotation | Source code |
| addCOSMICmouseHomologs | Source code |
| addCall | Source code |
| addChromosomeLines | Source code |
| addClinvarAnnotation | Source code |
| addMostSevereHit | Source code |
| addNullAnnotation | Source code |
| addPointMutations | Source code |
| addStream | Source code |
| addStreamSegment | Source code |
| addSubclone | Source code |
| addTheoreticalCNVerrors | Source code |
| addVAnullAnnotation | Source code |
| adjustBG | Source code |
| allCalls | Source code |
| alternativeFrequency | Source code |
| analyse | Man page Source code |
| annotateQ | Man page Source code |
| annotateSomaticQs | Man page Source code |
| annotationColumns | Source code |
| annotationToChr | Source code |
| annotationToX | Source code |
| annotationToX1X2 | Source code |
| bamToPileup | Man page Source code |
| bamToVariants | Source code |
| baseScore | Source code |
| baseStrength | Source code |
| batchToAnalysisDirectory | Source code |
| bestGuess | Source code |
| blurN | Source code |
| boostCRwidth | Source code |
| boostCRwidthRNA | Source code |
| bringAnnotation | Source code |
| callCNVs | Source code |
| callCancerNormalCNVs | Source code |
| callCloneTofM | Source code |
| callConsistencies | Source code |
| callConsistency | Source code |
| callConsistencyNumeric | Source code |
| callPrior | Source code |
| callToColHeatmap | Source code |
| callToColMaypole | Source code |
| callTofM | Source code |
| calledFromSingleSNP | Source code |
| callsToColMaypole | Source code |
| captureRegionToAnnotation | Source code |
| captureRegionsToBQoffset | Source code |
| captureRegionsToBed | Source code |
| captureRegionsToGenome | Source code |
| captureRegionsToNormalPath | Source code |
| checkForMissedLOH | Source code |
| checkRelatedness | Source code |
| checkRelatednessCrossBatch | Source code |
| checkSystem | Source code |
| chrLengths | Man page Source code |
| chrToX | Man page Source code |
| cleanVariantRownames | Source code |
| cleanVariants | Source code |
| cloneStoryRMS | Source code |
| cloneToCol | Source code |
| clonesInTree | Source code |
| clusterToConsistencies | Source code |
| cnvsToStories | Source code |
| cohortAnalyseBatch | Man page Source code |
| cohortAnalyseBatchContrast | Man page Source code |
| cohortGeneScore | Source code |
| colmeans | Source code |
| colorGradient | Source code |
| colsums | Source code |
| combineStories | Source code |
| compareGroups | Man page Source code |
| convertVariantsToVCF | Source code |
| correctForGeneSize | Source code |
| correctedFrequency | Source code |
| createDirectories | Source code |
| createOfflineTxDbs | Source code |
| defaultSuperParameters | Man page Source code |
| defaultSuperRuntimeSettings | Man page Source code |
| defaultSuperSettings | Man page Source code |
| deleteDebugFiles | Source code |
| dibaseScore | Source code |
| dibaseStrength | Source code |
| doPlotBayes | Source code |
| downloadCaptureRegions | Source code |
| downloadFile | Source code |
| downloadSuperFreqAnnotation | Source code |
| downloadSuperFreqCOSMIC | Source code |
| downloadSuperFreqDbSNP | Source code |
| downloadSuperFreqSignatures | Source code |
| downloadTemplate | Man page Source code |
| dumpInput | Man page Source code |
| enforceTransitive | Source code |
| ensureDirectoryExists | Source code |
| excludeClonesFromTree | Source code |
| expandFlags | Source code |
| explainSuperCaptureRegions | Source code |
| explainSuperDbSNPdirectory | Source code |
| explainSuperMetaData | Source code |
| explainSuperNormalDirectory | Source code |
| explainSuperReference | Source code |
| extractClonalities | Source code |
| extractqBAF | Source code |
| fillInMissingVariants | Source code |
| findBamWithBai | Source code |
| findChildren | Source code |
| findCloneTree | Source code |
| findCorrespondingNormal | Source code |
| findFinishedCohortIndividuals | Source code |
| findGLFC | Source code |
| findGLFCandPV | Source code |
| findGoI | Source code |
| findLocalCNV | Source code |
| findMirror | Source code |
| findReferenceBams | Source code |
| findSNPclonalities | Source code |
| findSNPstories | Source code |
| findShift | Source code |
| findShiftManually | Source code |
| findSubclones | Source code |
| fisherTest | Source code |
| fixFalseSNPcall | Source code |
| flagFromNormals | Source code |
| forceMerge | Source code |
| forceRedoEverything | Man page Source code |
| forceRedoNothing | Man page Source code |
| fragmentLength | Source code |
| freqToDirectionProb | Source code |
| frequencyError | Source code |
| generateBody | Source code |
| generateCnaTab | Source code |
| generateHead | Source code |
| generateHtml | Source code |
| generateNullFit | Source code |
| generateOverviewTab | Source code |
| generateRiverTab | Source code |
| generateScatterTab | Source code |
| generateScript | Source code |
| generateTabs | Source code |
| genomeToAssembly | Source code |
| genomeToMPgenome | Source code |
| get104profile | Man page Source code |
| get96signature | Source code |
| getAllIndividualVariants | Source code |
| getAllVEPdata | Source code |
| getBestSigma | Source code |
| getCNV | Source code |
| getCNVrates | Source code |
| getCNVstories | Source code |
| getCOSMICcensusGenes | Source code |
| getCohortCNAmatrix | Source code |
| getCohortMutationMatrix | Man page Source code |
| getCohortSNVmatrix | Source code |
| getCorrectedCR | Source code |
| getCosmicCensusDensity | Source code |
| getCosmicCounts | Man page Source code |
| getDeviation | Source code |
| getDodgyness | Source code |
| getFit | Source code |
| getFlatPrior | Source code |
| getHetRatio | Source code |
| getIndelSignature | Source code |
| getIndividualSmallVariants | Source code |
| getIndividualVariants | Source code |
| getMaxCov | Source code |
| getMeanCNV | Source code |
| getMoreVEPinfo | Man page Source code |
| getNormalVariant | Source code |
| getNormalVariants | Source code |
| getPosterior | Source code |
| getPriorNullDeviation | Source code |
| getPriors | Source code |
| getProjectVariants | Source code |
| getProjects | Source code |
| getQuality | Source code |
| getRownamesFor96signatures | Source code |
| getSNVrates | Source code |
| getSettings | Man page Source code |
| getStories | Man page Source code |
| getSubgroups | Source code |
| getSystematicVariance | Source code |
| getTheoreticalError | Source code |
| getVariant | Source code |
| getVariantsByIndividual | Man page Source code |
| getWBreaks | Source code |
| heatmapStories | Source code |
| hg38ChrLengths | Source code |
| humanAllChrLengths | Source code |
| humanChrLengths | Source code |
| identifyTooLowHetRatio | Source code |
| importCOSMICsignatures | Source code |
| importCaptureRegions | Man page Source code |
| importEnsemblData | Source code |
| importMutagenSignatures | Source code |
| importQualityScores | Source code |
| importReferenceGenome | Source code |
| importSampleMetaData | Man page Source code |
| importTCGAsignatures | Source code |
| inGene | Source code |
| inProject | Source code |
| inSubgroup | Source code |
| interpolate | Source code |
| interpolates | Source code |
| isAB | Source code |
| isCNV | Source code |
| isSaneMetaData | Source code |
| libNorm | Source code |
| linkBams | Source code |
| loadAndPlotProfiles | Source code |
| loadAnyCaptureRegions | Source code |
| loadClusterList | Source code |
| loadCohortMethods | Source code |
| loadData | Man page Source code |
| loadQsList | Source code |
| loessNorm | Source code |
| loessNormAll | Source code |
| loessNormAllToReference | Source code |
| loessNormToReference | Source code |
| makeCNAbatchHeatmap | Source code |
| makeCNAheatmap | Source code |
| makeCNVplots | Source code |
| makeCSVofAllPointMutations | Source code |
| makeCaptureFromFeatureCountRegions | Source code |
| makeCloneScatterPlots | Source code |
| makeFitPlots | Man page Source code |
| makeFitPlots2 | Source code |
| makeHeatmap | Man page Source code |
| makeMetaData | Source code |
| makeMetaDataFromBatch | Source code |
| makeRiverPlots | Source code |
| makeSNPprogressionPlots | Source code |
| makeScatterPlots | Source code |
| makeSummaryPlot | Source code |
| makeTreeConsistent | Source code |
| makepHeatmap | Man page Source code |
| markSomatics | Source code |
| matchFlagVariants | Source code |
| matchInternalQs | Source code |
| matchQs | Source code |
| matchToExac | Source code |
| matchTodbSNPs | Source code |
| matchVariants | Source code |
| mcri | Man page Source code |
| meanDistribution | Source code |
| mergeBatches | Man page Source code |
| mergeChromosomes | Source code |
| mergeDoubleLoss | Source code |
| mergeRegions | Source code |
| mergeStories | Source code |
| mergeStrs | Source code |
| mergeToOneRegion | Source code |
| mergeVariantList | Source code |
| metaToSamplePairs | Source code |
| metaToTimeSeries | Source code |
| mirrorDown | Source code |
| moreVEPnames | Man page Source code |
| mouseChrLengths | Source code |
| multiBlur | Source code |
| nameCaptureRegions | Source code |
| newBamToVariants | Source code |
| newFlagFromNormals | Source code |
| newVariants | Source code |
| noneg | Source code |
| normaliseCoverage | Source code |
| normaliseCoverageToHets | Source code |
| outputData | Source code |
| outputMeanCNV | Source code |
| outputNewVariants | Source code |
| outputSomaticVariants | Source code |
| pBinom | Source code |
| pToSigma | Source code |
| pTwoBinom | Source code |
| pairScore | Source code |
| parseMutagenSignatures | Source code |
| pasteLines | Source code |
| performPreliminaryVariantCallingOnMissingVCFs | Source code |
| plot104profilesByClone | Source code |
| plot104profilesBySample | Source code |
| plotBayesPDFs | Source code |
| plotCNAbatchHeatmap | Source code |
| plotCNAheatmap | Source code |
| plotCNAheatmapOverGoI | Man page Source code |
| plotCNAheatmapWithGoI | Man page Source code |
| plotCR | Man page Source code |
| plotClones | Source code |
| plotCohortMutationHeatmap | Man page Source code |
| plotColourScatter | Man page Source code |
| plotFrequencyDiagnostics | Source code |
| plotHR | Source code |
| plotMA | Man page Source code |
| plotMAFLFC | Source code |
| plotMeanCNV | Source code |
| plotMeanCNVtoFile | Source code |
| plotMultipageMutationMatrix | Source code |
| plotMutationMatrix | Source code |
| plotPost | Source code |
| plotProfiles | Source code |
| plotRiver | Man page Source code |
| plotShiftedMAFLFC | Source code |
| plotShrunk | Source code |
| plotSimilarSignatures | Source code |
| plotStories | Man page Source code |
| plotSubgroupCNVtoFile | Source code |
| plotSubgroupMutationMatrix | Source code |
| plotSummary | Source code |
| plotVolcano | Source code |
| plotXRank | Source code |
| postAnalyseVEP | Man page Source code |
| postProcess | Source code |
| postRank | Source code |
| postWidth | Source code |
| posteriors | Source code |
| preprocessCCGD | Source code |
| preprocessClinvar | Source code |
| printHTML | Man page Source code |
| projectMeanCNV | Source code |
| propagateForceRedo | Source code |
| qToGR | Source code |
| qToGRanges | Man page Source code |
| qToVCF | Source code |
| qsToGRL | Source code |
| qualityProgression | Source code |
| qualityScatter | Man page Source code |
| randomCol | Source code |
| randomCols | Source code |
| randomLtys | Source code |
| rangesToBindingScore | Source code |
| readsToPileup | Source code |
| redoHetCalculations | Source code |
| refBias | Source code |
| refBiasMirror | Source code |
| refUnbias | Source code |
| regionalGCcorrect | Source code |
| removeChrFromDump | Source code |
| renameCloneTree | Source code |
| renameClones | Source code |
| renameGoIs | Source code |
| reorderStories | Source code |
| requireFileExists | Man page Source code |
| resetMargins | Source code |
| reverseCall | Source code |
| rowmeans | Source code |
| rowsums | Source code |
| runDE | Man page Source code |
| runSummaryPostAnalysis | Man page Source code |
| runVEP | Man page Source code |
| sameCNV | Source code |
| sameCallAsNeighbour | Source code |
| sameClone | Source code |
| sampleToIndividual | Source code |
| sampleToRdir | Source code |
| samplesToRdirs | Source code |
| saveMetaData | Source code |
| scalarNorm | Source code |
| scoreConsistencies | Source code |
| selectGermlineHets | Source code |
| selectGermlineHetsFromCancer | Source code |
| selectedProtectedHets | Source code |
| setVariantLoss | Source code |
| setupCohortPlot | Source code |
| severityToType | Man page Source code |
| shareSNPs | Source code |
| shareVariants | Source code |
| shortenCalls | Source code |
| solveCigars | Source code |
| splitEvents | Source code |
| splitMeanCNV | Source code |
| splitMetaData | Source code |
| splitRegions | Source code |
| spreadPositions | Source code |
| spreadPositions2D | Source code |
| storiesToCloneStories | Source code |
| storyToLabel | Source code |
| stoufferTest | Source code |
| subsetFit | Source code |
| superCohort | Man page Source code |
| superFreq | Man page Source code |
| superInputFiles | Man page Source code |
| superOutputDirectories | Man page Source code |
| superVersion | Man page Source code |
| third | Source code |
| topXRank | Source code |
| trimVariantsByIndividual | Source code |
| twoBinom | Source code |
| typeToSeverity | Man page Source code |
| unifyCaptureRegions | Source code |
| updateCNVplots | Source code |
| updateDeletions | Source code |
| updateInsertions | Source code |
| updateMultisamplePlots | Source code |
| updateScatterPlots | Source code |
| updateStory | Source code |
| vafScatter | Man page Source code |
| variantLoss | Source code |
| vcfToPositions | Source code |
| vecNorm | Source code |
| whichDistribution | Source code |
| whichUnitarityViolating | Source code |
| writeToVCF | Man page Source code |
| xToChr | Man page Source code |
| xToGene | Man page Source code |
| xToGeneFromDB | Source code |
| xToPos | Man page Source code |
