Name Mode Size
..
FastQStreamer.getReads.Rd 100644 0 kb
FastQStreamer.init.Rd 100644 1 kb
FastQStreamer.release.Rd 100644 0 kb
HTSeqGenie.Rd 100755 2 kb
TP53GenomicFeatures.Rd 100644 1 kb
alignReads.Rd 100644 0 kb
alignReadsChunk.Rd 100644 1 kb
analyzeVariants.Rd 100644 0 kb
annotateVariants.Rd 100644 0 kb
bamCountUniqueReads.Rd 100644 0 kb
buildConfig.Rd 100644 1 kb
buildGenomicFeaturesFromTxDb.Rd 100644 1 kb
buildShortReadReports.Rd 100755 0 kb
buildTP53FastaGenome.Rd 100644 0 kb
buildTP53GenomeTemplate.Rd 100644 0 kb
buildTallyParam.Rd 100755 0 kb
calculateCoverage.Rd 100644 0 kb
calculateTargetLengths.Rd 100644 1 kb
callVariantsGATK.Rd 100755 0 kb
checkConfig.Rd 100644 0 kb
checkGATKJar.Rd 100755 0 kb
checkPicardJar.Rd 100644 1 kb
computeBamStats.Rd 100644 0 kb
computeCoverage.Rd 100644 1 kb
countFeatures.Rd 100644 1 kb
countGenomicFeatures.Rd 100644 0 kb
countGenomicFeaturesChunk.Rd 100644 1 kb
createTmpDir.Rd 100644 1 kb
detectAdapterContam.Rd 100644 1 kb
detectQualityInFASTQFile.Rd 100644 1 kb
detectRRNA.Rd 100644 1 kb
excludeVariantsByRegions.Rd 100755 1 kb
filterByLength.Rd 100755 1 kb
filterQuality.Rd 100644 1 kb
findVariantFile.Rd 100755 1 kb
gatk.Rd 100755 1 kb
generateSingleGeneDERs.Rd 100644 1 kb
getAdapterSeqs.Rd 100644 1 kb
getBams.Rd 100644 0 kb
getChunkDirs.Rd 100644 0 kb
getConfig.Rd 100644 1 kb
getConfig.integer.Rd 100644 1 kb
getConfig.logical.Rd 100644 0 kb
getConfig.numeric.Rd 100644 0 kb
getConfig.vector.Rd 100755 0 kb
getEndNumber.Rd 100644 0 kb
getMemoryUsage.Rd 100644 0 kb
getNumberOfReadsInFASTQFile.Rd 100644 0 kb
getNumericVectorDataFromFile.Rd 100644 0 kb
getObjectFilename.Rd 100644 1 kb
getPackageFile.Rd 100644 1 kb
getRRNAIds.Rd 100644 1 kb
getRandomAlignCutoff.Rd 100644 0 kb
getTabDataFromFile.Rd 100644 1 kb
getTraceback.Rd 100644 0 kb
hashCoverage.Rd 100644 0 kb
hashVariants.Rd 100644 0 kb
hashVector.Rd 100644 0 kb
initDirs.Rd 100644 0 kb
initLog.Rd 100644 0 kb
initLogger.Rd 100644 0 kb
initPipelineFromConfig.Rd 100644 0 kb
initPipelineFromSaveDir.Rd 100644 1 kb
isAboveQualityThresh.Rd 100644 1 kb
isAdapter.Rd 100644 1 kb
isConfig.Rd 100644 0 kb
isFirstFragment.Rd 100644 1 kb
isSparse.Rd 100755 1 kb
listIterator.init.Rd 100644 0 kb
listIterator.next.Rd 100644 0 kb
loadConfig.Rd 100644 0 kb
logdebug.Rd 100644 0 kb
logerror.Rd 100755 0 kb
loginfo.Rd 100644 0 kb
logwarn.Rd 100644 0 kb
makeDir.Rd 100644 0 kb
makeRandomSreads.Rd 100755 0 kb
markDuplicates.Rd 100644 1 kb
markDups.Rd 100644 0 kb
mergeAlignReads.Rd 100644 1 kb
mergeCoverage.Rd 100644 1 kb
mergeLanes.Rd 100644 1 kb
mergePreprocessReads.Rd 100644 1 kb
mergeSummaryAlignment.Rd 100644 1 kb
parseDCF.Rd 100644 1 kb
parseSummaries.Rd 100644 1 kb
picard.Rd 100644 1 kb
plotDF.Rd 100644 1 kb
preprocessReads.Rd 100644 1 kb
preprocessReadsChunk.Rd 100755 0 kb
processChunks.Rd 100644 1 kb
readInputFiles.Rd 100644 0 kb
readRNASeqEnds.Rd 100644 1 kb
realignIndels.Rd 100644 0 kb
realignIndelsGATK.Rd 100644 1 kb
relativeBarPlot.Rd 100644 1 kb
removeChunkDir.Rd 100644 0 kb
resource.Rd 100644 0 kb
rpkm.Rd 100644 0 kb
runAlignment.Rd 100644 1 kb
runPipeline.Rd 100644 2 kb
runPipelineConfig.Rd 100644 1 kb
runPreprocessReads.Rd 100644 1 kb
safe.yield.Rd 100755 0 kb
safeExecute.Rd 100644 1 kb
safeGetObject.Rd 100755 0 kb
safeUnlink.Rd 100644 0 kb
saveWithID.Rd 100644 1 kb
sclapply.Rd 100644 1 kb
setChunkDir.Rd 100644 0 kb
setUpDirs.Rd 100644 1 kb
setupTestFramework.Rd 100644 1 kb
statCountFeatures.Rd 100644 1 kb
traceMem.Rd 100644 0 kb
trimReads.Rd 100644 1 kb
trimTailsByQuality.Rd 100755 1 kb
truncateReads.Rd 100644 1 kb
tryKeepTraceback.Rd 100644 0 kb
updateConfig.Rd 100644 0 kb
vcfStat.Rd 100755 0 kb
wrap.callVariants.Rd 100755 0 kb
writeAudit.Rd 100644 0 kb
writeConfig.Rd 100644 0 kb
writeFastQFiles.Rd 100644 0 kb
writeFeatureCountsHTML.Rd 100755 1 kb
writeGenomicFeaturesReport.Rd 100644 0 kb
writePreprocessAlignHTML.Rd 100755 1 kb
writePreprocessAlignReport.Rd 100644 0 kb
writeSummary.Rd 100644 1 kb
writeVCF.Rd 100644 0 kb