| .. |
|
|
| 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 |
