API for HTSeqGenie
A NGS analysis pipeline.
| Global functions | |
|---|---|
| .IDverify | Source code |
| .calcExonsCovered | Source code |
| .calcGenomicFeaturesDetected | Source code |
| .calcHitsByGenomicFeature | Source code |
| .callGenotypes | Source code |
| .createQAReport | Source code |
| .finalCallFromIndividualQACalls | Source code |
| .generateCountFeaturesPlots | Source code |
| .getAllSummaries | Source code |
| .getEffectiveReadLengths | Source code |
| .makePreprocessAlignPlots | Source code |
| .makeReadFiltering | Source code |
| .onLoad | Source code |
| .plot.in.out.min.max.readlength | Source code |
| .plot.perc.reads.bad | Source code |
| .plot.perc.reads.good | Source code |
| .plot.quartile.target.length | Source code |
| .plot.reads.bad | Source code |
| .plot.reads.good | Source code |
| .plotAlignmentSummary | Source code |
| .plotBamStatsSummary | Source code |
| .plotCountGFSummary | Source code |
| .plotCountGFbyFeatureSummary | Source code |
| .plotGenesDetected | Source code |
| .plotJunctionReads | Source code |
| .plotPreprocessSummary | Source code |
| .plotReadMappingsPerChr | Source code |
| .plotVariantsSummary | Source code |
| .postFilterVariants | Source code |
| .reportFailedRuns | Source code |
| .saveVTvars | Source code |
| .zipUp | Source code |
| FastQStreamer.getReads | Man page Source code |
| FastQStreamer.init | Man page Source code |
| FastQStreamer.release | Man page Source code |
| HTSeqGenie | Man page |
| TP53GenomicFeatures | Man page Source code |
| addHandler | Source code |
| alignReads | Man page Source code |
| alignReadsChunk | Man page Source code |
| analyzeVariants | Man page Source code |
| annotateVariants | Man page Source code |
| bamCountUniqueReads | Man page Source code |
| buildAnalyzedBam | Source code |
| buildAnyFastaGenome | Source code |
| buildCallingFilters | Source code |
| buildConfig | Man page Source code |
| buildGenomicFeaturesFromTxDb | Man page Source code |
| buildGsnapArgs | Source code |
| buildGsnapParams | Source code |
| buildShortReadReports | Man page Source code |
| buildTP53FastaGenome | Man page Source code |
| buildTP53GenomeTemplate | Man page Source code |
| buildTallyParam | Man page Source code |
| calculateCoverage | Man page Source code |
| calculateTargetLengths | Man page Source code |
| callVariantsGATK | Man page Source code |
| callVariantsVariantTools | Source code |
| catBams | Source code |
| checkConfig | Man page Source code |
| checkConfig.GATK | Source code |
| checkConfig.alignReads | Source code |
| checkConfig.analyzeVariants | Source code |
| checkConfig.analyzeVariants.VT | Source code |
| checkConfig.coverage | Source code |
| checkConfig.debug | Source code |
| checkConfig.detectAdapterContam | Source code |
| checkConfig.detectRRNA | Source code |
| checkConfig.filterQuality | Source code |
| checkConfig.input | Source code |
| checkConfig.markDuplicates | Source code |
| checkConfig.noextraparameters | Source code |
| checkConfig.output | Source code |
| checkConfig.realignIndels | Source code |
| checkConfig.shortReadReport | Source code |
| checkConfig.system | Source code |
| checkConfig.template | Source code |
| checkConfig.trimReads | Source code |
| checkGATKJar | Man page Source code |
| checkInputConfigs | Source code |
| checkPicardJar | Man page Source code |
| checkVEP | Source code |
| computeBamStats | Man page Source code |
| computeCoverage | Man page Source code |
| computeCoverageStats | Source code |
| computeWidth | Source code |
| countFeatures | Man page Source code |
| countGenomicFeatures | Man page Source code |
| countGenomicFeaturesChunk | Man page Source code |
| create.result.link.table | Source code |
| createSummaryAlignment | Source code |
| createSummaryCounts | Source code |
| createTmpDir | Man page Source code |
| detectAdapterContam | Man page Source code |
| detectQualityInFASTQFile | Man page Source code |
| detectRRNA | Man page |
| doMergeLanes | Source code |
| dotboxplot | Source code |
| estimateCutoffs | Source code |
| estimateFragmentLength | Source code |
| excludeVariantsByRegions | Man page Source code |
| filterByLength | Man page Source code |
| filterGATKVars | Source code |
| filterQuality | Man page Source code |
| findTemplate | Source code |
| findVariantFile | Man page Source code |
| gatk | Man page Source code |
| generateSingleGeneDERs | Man page Source code |
| get.random.chunk.dir.name | Source code |
| getAdapterSeqs | Man page Source code |
| getAnalyzedBamFile | Source code |
| getBamType | Source code |
| getBams | Man page Source code |
| getChunkDirs | Man page Source code |
| getConfig | Man page Source code |
| getConfig.integer | Man page Source code |
| getConfig.logical | Man page Source code |
| getConfig.numeric | Man page Source code |
| getConfig.vector | Man page Source code |
| getEndNumber | Man page Source code |
| getGenomeSegments | Source code |
| getGmapGenome | Source code |
| getMemoryUsage | Man page Source code |
| getNumberOfReadsInFASTQFile | Man page Source code |
| getNumericVectorDataFromFile | Man page Source code |
| getObjectFilename | Man page Source code |
| getPackageFile | Man page Source code |
| getRRNAIds | Man page |
| getRandomAlignCutoff | Man page Source code |
| getTabDataFromFile | Man page Source code |
| getTraceback | Man page Source code |
| hashCoverage | Man page Source code |
| hashVariants | Man page Source code |
| hashVector | Man page Source code |
| how_many | Source code |
| initDirs | Man page Source code |
| initLog | Man page Source code |
| initLogger | Man page Source code |
| initPipelineFromConfig | Man page Source code |
| initPipelineFromSaveDir | Man page Source code |
| isAboveQualityThresh | Man page Source code |
| isAdapter | Man page Source code |
| isConfig | Man page Source code |
| isFirstFragment | Man page Source code |
| isSparse | Man page Source code |
| listIterator.init | Man page Source code |
| listIterator.next | Man page Source code |
| loadConfig | Man page Source code |
| logReset | Source code |
| logdebug | Man page Source code |
| logerror | Man page Source code |
| loginfo | Man page Source code |
| loglevel | Source code |
| logwarn | Man page Source code |
| makeDir | Man page Source code |
| makeRandomSreads | Man page Source code |
| markDuplicates | Man page Source code |
| markDups | Man page Source code |
| mergeAlignReads | Man page Source code |
| mergeBAMsAcrossDirs | Source code |
| mergeBams | Source code |
| mergeCountGenomicFeatures | Source code |
| mergeCounts | Source code |
| mergeCoverage | Man page Source code |
| mergeLanes | Man page Source code |
| mergePreprocessReads | Man page Source code |
| mergeSummaryAlignment | Man page Source code |
| mergeSummaryCounts | Source code |
| mergeSummaryPreprocess | Source code |
| parseDCF | Man page Source code |
| parseSummaries | Man page Source code |
| picard | Man page Source code |
| plotDF | Man page Source code |
| plot_hist | Source code |
| postMergeChecks | Source code |
| preMergeChecks | Source code |
| preprocessReads | Man page Source code |
| preprocessReadsChunk | Man page Source code |
| processChunks | Man page Source code |
| readInputFiles | Man page Source code |
| readRNASeqEnds | Man page Source code |
| realignIndels | Man page Source code |
| realignIndelsGATK | Man page Source code |
| realignOne | Source code |
| relativeBarPlot | Man page Source code |
| removeChunkDir | Man page Source code |
| resource | Man page Source code |
| rpkm | Man page |
| runAlignment | Man page Source code |
| runPipeline | Man page Source code |
| runPipelineConfig | Man page Source code |
| runPreprocessReads | Man page Source code |
| safe.file.rename | Source code |
| safe.yield | Man page Source code |
| safeExecute | Man page Source code |
| safeGetObject | Man page Source code |
| safeUnlink | Man page Source code |
| sanityCheck | Source code |
| saveCoverage | Source code |
| saveWithID | Man page Source code |
| sclapply | Man page Source code |
| setChunkDir | Man page Source code |
| setLevel | Source code |
| setUpDirs | Man page Source code |
| setupTestFramework | Man page Source code |
| statCountFeatures | Man page Source code |
| traceMem | Man page Source code |
| trimReads | Man page |
| trimTailsByQuality | Man page |
| truncateReads | Man page Source code |
| tryKeepTraceback | Man page Source code |
| updateConfig | Man page Source code |
| vcfStat | Man page Source code |
| wrap.callVariants | Man page Source code |
| wrapGsnap | Source code |
| writeAudit | Man page Source code |
| writeConfig | Man page Source code |
| writeFastQFiles | Man page |
| writeFeatureCountsHTML | Man page Source code |
| writeGenomicFeaturesReport | Man page Source code |
| writePreprocessAlignHTML | Man page Source code |
| writePreprocessAlignReport | Man page Source code |
| writeSummary | Man page Source code |
| writeVCF | Man page Source code |
