API for HTSeqGenie
A NGS analysis pipeline.

Global functions
FastQStreamer.getReads Man page Source code
FastQStreamer.init Man page Source code
FastQStreamer.release Man page Source code
HTSeqGenie Man page
IDverify Source code
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
calcExonsCovered Source code
calcGenomicFeaturesDetected Source code
calcHitsByGenomicFeature Source code
calculateCoverage Man page Source code
calculateTargetLengths Man page Source code
callGenotypes 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.countGenomicFeatures 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
createQAReport 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 Source code
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
finalCallFromIndividualQACalls Source code
findTemplate Source code
findVariantFile Man page Source code
gatk Man page Source code
generateCountFeaturesPlots Source code
generateSingleGeneDERs Man page Source code
get.random.chunk.dir.name Source code
getAdapterSeqs Man page Source code
getAllSummaries 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
getEffectiveReadLengths 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 Source code
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
heatmap 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
makePreprocessAlignPlots Source code
makeRandomSreads Man page Source code
makeReadFiltering 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
mergeDetectAdapterContam Source code
mergeLanes Man page Source code
mergePreprocessReads Man page Source code
mergePreprocessedFastQ Source code
mergeSummaryAlignment Man page Source code
mergeSummaryCounts Source code
mergeSummaryPreprocess Source code
onLoad Source code
parseDCF Man page Source code
parseSummaries Man page Source code
picard Man page 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
plotDF Man page Source code
plotGenesDetected Source code
plotJunctionReads Source code
plotPreprocessSummary Source code
plotReadMappingsPerChr Source code
plotVariantsSummary Source code
plot_hist Source code
postFilterVariants 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
reportFailedRuns Source code
resource Man page Source code
rpkm Man page Source code
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
saveVTvars 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 Source code
trimTailsByQuality Man page Source code
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 Source code
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
writeToConsole Source code
writeToFile Source code
writeVCF Man page Source code
zipUp Source code
HTSeqGenie documentation built on Nov. 2, 2018, 6:01 p.m.