API for HenrikBengtsson/aroma.seq
High-Throughput Sequence Analysis using the Aroma Framework

Global functions
AbstractAlignment Man page
AbstractIndexFile Man page
AbstractIndexSet Man page
AbstractIndexSet.getDefaultFilePatterns Man page
AromaPathnameInterface Man page
AromaSeq Man page
AromaSeq$capabilitiesOf Man page
AromaSeq.capabilitiesOf Man page
AromaSeq.isCapableOf Man page
AromaSeqDataFile Man page
AromaSeqDataFileSet Man page
AromaSeqTransform Man page
AromaUncFile Man page
AromaUnitNucleotideCountsFile Man page
BamDataFile Man page
BamDataFile.validate Man page
BamDataSet Man page
BamDownsampler Man page
BamIndexDataFile Man page
BamMerger Man page
BinnedGcNormalization Man page
Bowtie2Alignment Man page
Bowtie2Alignment.process Man page
Bowtie2IndexFile Man page
Bowtie2IndexSet Man page
Bowtie2IndexSet.buildTopHat2TranscriptomeIndexSet Man page
Bowtie2IndexSet.getDefaultFilePatterns Man page
Bowtie2IndexSet.readSeqLengths Man page
BwaAlignment Man page
BwaAlignment.process Man page
BwaIndexFile Man page
BwaIndexSet Man page
BwaIndexSet.as.character Man page
BwaIndexSet.getDefaultFilePatterns Man page
BwaIndexSet.getSeqLengths Man page
BwaIndexSet.getSeqNames Man page
BwaIndexSet.isCompatibleWith Man page
BwaIndexSet.isComplete Man page
BwaIndexSet.readAnnData Man page
CnvKitCopyNumberRatioFile Man page
CnvKitCopyNumberRatioFileSet Man page
FastQCDataFile Man page
FastQCDataFileSet Man page
FastQCReporter Man page
FastaReferenceFile Man page
FastaReferenceFile$byOrganism Man page
FastaReferenceFile.buildBowtie2IndexSet Man page
FastaReferenceFile.buildBwaIndexSet Man page
FastaReferenceFile.buildDictionary Man page
FastaReferenceFile.buildIndex Man page
FastaReferenceFile.byOrganism Man page
FastaReferenceFile.findByOrganism Man page
FastaReferenceIndexFile Man page
FastaReferenceSet Man page
FastaReferenceSet.writeFastaReferenceFile Man page
FastqDataFile Man page
FastqDataSet Man page
FastqDownsampler Man page
FastqQualityReport Man page
FileGroupsInterface Man page
GatkAlleleCounting Man page
GcBaseFile Man page
GtfDataFile Man page
GtfDataFile$byOrganism Man page
GtfDataFile.byOrganism Man page
GtfDataFile.findByOrganism Man page
HTSeqCountDataFile Man page
HTSeqCountDataSet Man page
HTSeqCountDataSet.extractDGEList Man page
HTSeqCountDataSet.readDGE Man page
HTSeqCounting Man page
IlluminaFastqDataFile Man page
IlluminaFastqDataSet Man page
MPileupFile Man page
MPileupFileSet Man page
Non-documented objects Man page
PairedEndFastqDataSet Man page
PicardDuplicateRemoval Man page
QDNAseqEstimation Man page
SamDataFile Man page
SamDataSet Man page
SamReadGroup Man page
SamTransform Man page
SequenceContigsInterface Man page
SeqzFile Man page
SeqzFileSet Man page
SraDataFile Man page
SraDataSet Man page
TopHat2Alignment Man page
TotalCnBinnedCounting Man page
agsub Man page
allocateFromUgp Man page
allocateFromUgp.AromaUnitNucleotideCountsFile Man page
anyDuplicated.AromaUgpFile Man page
aroma.seq Man page
aroma.seq-package Man page
as.character,BwaIndexSet-method Man page
as.character.AbstractAlignment Man page
as.character.AbstractIndexFile Man page
as.character.AbstractIndexSet Man page
as.character.AromaSeqTransform Man page
as.character.BamDataFile Man page
as.character.BamDataSet Man page
as.character.BamIndexDataFile Man page
as.character.BinnedGcNormalization Man page
as.character.Bowtie2Alignment Man page
as.character.Bowtie2IndexSet Man page
as.character.BwaAlignment Man page
as.character.BwaIndexFile Man page
as.character.BwaIndexSet Man page
as.character.FastQCDataFile Man page
as.character.FastaReferenceFile Man page
as.character.FastaReferenceIndexFile Man page
as.character.FastqDataFile Man page
as.character.FastqDataSet Man page
as.character.GcBaseFile Man page
as.character.GtfDataFile Man page
as.character.IlluminaFastqDataFile Man page
as.character.IlluminaFastqDataSet Man page
as.character.PicardDuplicateRemoval Man page
as.character.SamDataFile Man page
as.character.SamReadGroup Man page
as.character.SraDataFile Man page
asBwaString Man page
asBwaString.SamReadGroup Man page
asSamList Man page
asSamList.SamReadGroup Man page
asString Man page
asString.SamReadGroup Man page
assertNoCommas Man page
assertNoDuplicated Man page
assertNoSpaces Man page
assignBy Man page
assignBy.SamReadGroup Man page
bDebugSystemBowtie2Build Man page
binTabulate Man page
binTabulate.MaskedDNAString Man page
bowtie2 Man page
bowtie2Build Man page
bowtie2Build.default Man page
bowtie2IndexPrefix Man page
bowtie2IndexPrefix.default Man page
buildBowtie2IndexSet Man page
buildBowtie2IndexSet,FastaReferenceFile-method Man page
buildBowtie2IndexSet.FastaReferenceFile Man page
buildBwaIndexSet Man page
buildBwaIndexSet,FastaReferenceFile-method Man page
buildBwaIndexSet.FastaReferenceFile Man page
buildDictionary Man page
buildDictionary,FastaReferenceFile-method Man page
buildDictionary.FastaReferenceFile Man page
buildIndex Man page
buildIndex,FastaReferenceFile-method Man page
buildIndex.BamDataFile Man page
buildIndex.FastaReferenceFile Man page
buildTopHat2TranscriptomeIndexSet Man page
buildTopHat2TranscriptomeIndexSet,Bowtie2IndexSet-method Man page
buildTopHat2TranscriptomeIndexSet.Bowtie2IndexSet Man page
bwaAln Man page
bwaAln.default Man page
bwaIndex Man page
bwaIndex.FastaReferenceFile Man page
bwaIndex.default Man page
bwaIndexPrefix Man page
bwaIndexPrefix.default Man page
bwaSampe Man page
bwaSampe.default Man page
bwaSamse Man page
bwaSamse.default Man page
byName.BamDataSet Man page
byName.CnvKitCopyNumberRatioFileSet Man page
byName.FastqDataSet Man page
byName.HTSeqCountDataSet Man page
byName.SamDataSet Man page
byName.SeqzFileSet Man page
byName.SraDataSet Man page
byOrganism Man page
byOrganism,FastaReferenceFile-method Man page
byOrganism,GtfDataFile-method Man page
byOrganism.FastaReferenceFile Man page
byOrganism.GtfDataFile Man page
byPath.BamDataSet Man page
byPath.FastQCDataFileSet Man page
byPath.FastaReferenceSet Man page
byPath.FastqDataSet Man page
byPath.HTSeqCountDataSet Man page
byPath.PairedEndFastqDataSet Man page
byPath.SamDataSet Man page
byPath.SraDataSet Man page
byPrefix Man page
byPrefix.AbstractIndexSet Man page
byPrefix.BwaIndexSet Man page
byScanBamHeader Man page
byScanBamHeader.SamReadGroup Man page
capabilitiesOf Man page
capabilitiesOf,AromaSeq-method Man page
capabilitiesOf.AromaSeq Man page
cleanSeqNames Man page
cleanSeqNames.SequenceContigsInterface Man page
convertToBam Man page
convertToBam.SamDataFile Man page
convertToBam.SamDataSet Man page
convertToBamDataFile Man page
convertToBamDataFile.SamDataFile Man page
convertToBamDataSet Man page
convertToSam Man page
convertToSam.BamDataFile Man page
convertToSam.BamDataSet Man page
countNucleotides Man page
countNucleotides.BamDataFile Man page
countNucleotides.BamDataSet Man page
createIndexPrefix Man page
createIndexPrefix.default Man page
cuffdiff Man page
cuffdiff.default Man page
cufflinks Man page
cufflinks.default Man page
directoryItem Man page
directoryItem.GenericDataFile Man page
directoryItem.GenericDataFileSet Man page
directoryItems Man page
directoryItems.GenericDataFile Man page
directoryItems.GenericDataFileSet Man page
directoryItems.character Man page
directoryStructure Man page
directoryStructure.AromaPathnameInterface Man page
directoryStructure.AromaSeqDataFile Man page
directoryStructure.AromaSeqDataFileSet Man page
directoryStructure.BamDataFile Man page
directoryStructure.BamDataSet Man page
directoryStructure.FastqDataFile Man page
directoryStructure.FastqDataSet Man page
directoryStructure.GenericDataFile Man page
directoryStructure.GenericDataFileSet Man page
directoryStructure.NULL Man page
directoryStructure.SamDataFile Man page
directoryStructure.SamDataSet Man page
directoryStructure.character Man page
directoryStructure.list Man page
directoryStructure<- Man page
directoryStructure<-.GenericDataFile Man page
directoryStructure<-.GenericDataFileSet Man page
doBWA Man page
doBWA.AromaSeqDataFileSet Man page
doBWA.default Man page
doBowtie2 Man page
doBowtie2.FastqDataSet Man page
doBowtie2.default Man page
doDownsample Man page
doDownsample.BamDataSet Man page
doDownsample.FastqDataSet Man page
doDownsample.default Man page
doHTSeqCount Man page
doHTSeqCount.BamDataSet Man page
doHTSeqCount.default Man page
doQDNAseq Man page
doQDNAseq.BamDataFile Man page
doQDNAseq.BamDataSet Man page
doQDNAseq.FastqDataSet Man page
doQDNAseq.default Man page
doTopHat2 Man page
doTopHat2.FastqDataSet Man page
doTopHat2.default Man page
extractCounts Man page
extractCounts.HTSeqCountDataFile Man page
extractCounts.HTSeqCountDataSet Man page
extractDGEList Man page
extractDGEList,HTSeqCountDataSet-method Man page
extractDGEList.HTSeqCountDataSet Man page
extractRawCopyNumbers.BamDataFile Man page
extractReadStartPositions Man page
extractReadStartPositions.BamDataFile Man page
extractSamReadGroup Man page
extractSamReadGroup.FastqDataFile Man page
extractSamReadGroup.IlluminaFastqDataFile Man page
fastQC Man page
fastQC.default Man page
fastqDump Man page
fastqDump.SraDataFile Man page
fastqDump.SraDataSet Man page
fastqDump.default Man page
findBWA Man page
findBowtie2 Man page
findByName.BamDataSet Man page
findByName.CnvKitCopyNumberRatioFileSet Man page
findByName.FastqDataSet Man page
findByName.HTSeqCountDataSet Man page
findByName.MPileupFileSet Man page
findByName.SamDataSet Man page
findByName.SeqzFileSet Man page
findByName.SraDataSet Man page
findByOrganism Man page
findByOrganism,FastaReferenceFile-method Man page
findByOrganism,GtfDataFile-method Man page
findByOrganism.FastaReferenceFile Man page
findByOrganism.GtfDataFile Man page
findCNVkit Man page
findCmd Man page
findCmd.default Man page
findCmdv Man page
findCmdv.default Man page
findExternal Man page
findFastQC Man page
findFastqDump Man page
findFilesTodo Man page
findFilesTodo.AromaSeqTransform Man page
findFilesTodo.TotalCnBinnedCounting Man page
findGATK Man page
findHTSeq Man page
findJava Man page
findMateFile Man page
findMateFile.FastqDataFile Man page
findPerl Man page
findPicard Man page
findPython Man page
findRspReportTemplate Man page
findRspReportTemplate.FastqDataFile Man page
findRspReportTemplate.FastqDataSet Man page
findRspReportTemplate.Object Man page
findSamtools Man page
findSraToolkit Man page
findTopHat Man page
findTopHat1 Man page
findTopHat2 Man page
gatk Man page
gatk.default Man page
getAcronym Man page
getAcronym.AbstractAlignment Man page
getAcronym.AromaSeqTransform Man page
getAromaUncFile Man page
getAromaUncFile.AromaUgpFile Man page
getAsteriskTags.AbstractAlignment Man page
getAsteriskTags.AromaSeqTransform Man page
getAsteriskTags.BamDownsampler Man page
getAsteriskTags.BamMerger Man page
getAsteriskTags.BinnedGcNormalization Man page
getAsteriskTags.Bowtie2Alignment Man page
getAsteriskTags.BwaAlignment Man page
getAsteriskTags.FastQCReporter Man page
getAsteriskTags.FastqDownsampler Man page
getAsteriskTags.PicardDuplicateRemoval Man page
getAsteriskTags.QDNAseqEstimation Man page
getAsteriskTags.TopHat2Alignment Man page
getBarcodeSequence Man page
getBarcodeSequence.IlluminaFastqDataFile Man page
getBinWidth Man page
getBinWidth.QDNAseqEstimation Man page
getChipType.BamDataFile Man page
getChipType.BamDataSet Man page
getColumnNames.AromaUnitNucleotideCountsFile Man page
getCombineBy Man page
getCombineBy.GatkAlleleCounting Man page
getCommonSeqWidth Man page
getCommonSeqWidth.FastqDataFile Man page
getDataSetName Man page
getDataSetName.GenericDataFile Man page
getDefaultColumnClassPatterns.CnvKitCopyNumberRatioFile Man page
getDefaultColumnClassPatterns.SeqzFile Man page
getDefaultColumnNames.AromaUnitNucleotideCountsFile Man page
getDefaultFilePatterns Man page
getDefaultFilePatterns,AbstractIndexSet-method Man page
getDefaultFilePatterns,Bowtie2IndexSet-method Man page
getDefaultFilePatterns,BwaIndexSet-method Man page
getDefaultFilePatterns.AbstractIndexSet Man page
getDefaultFilePatterns.Bowtie2IndexSet Man page
getDefaultFilePatterns.BwaIndexSet Man page
getDefaultFullName.AromaSeqDataFile Man page
getDefaultFullName.AromaSeqDataFileSet Man page
getDefaultFullName.FastQCDataFile Man page
getDefaultFullName.FastaReferenceFile Man page
getDefaultFullName.FastaReferenceIndexFile Man page
getDefaultFullName.FastqDataFile Man page
getDefaultFullName.MPileupFile Man page
getDefaultFullName.SeqzFile Man page
getDefaultSamReadGroup Man page
getDefaultSamReadGroup.FastqDataFile Man page
getDefaultSamReadGroup.FastqDataSet Man page
getDefaultSamReadGroup.IlluminaFastqDataFile Man page
getDepth.BamDataSet Man page
getDepth.FastaReferenceSet Man page
getDepth.FastqDataSet Man page
getDepth.HTSeqCountDataSet Man page
getDepth.SamDataSet Man page
getDepth.SraDataSet Man page
getExpectedOutputFullnames.GatkAlleleCounting Man page
getExpectedOutputFullnames.TotalCnBinnedCounting Man page
getExpectedOutputPaths Man page
getExpectedOutputPaths.TopHat2Alignment Man page
getExtensionPattern.AromaUnitNucleotideCountsFile Man page
getExternalHome Man page
getFastaReferenceFile Man page
getFastaReferenceFile.AbstractIndexSet Man page
getFilePairs Man page
getFilePairs.FastqDataSet Man page
getFileVersion Man page
getFileVersion.IlluminaFastqDataFile Man page
getFilenameExtension.AromaUnitNucleotideCountsFile Man page
getFilenameExtension.BamDataFile Man page
getFirstSequenceInfo Man page
getFirstSequenceInfo.IlluminaFastqDataFile Man page
getFlagStat Man page
getFlagStat.BamDataFile Man page
getFlavor Man page
getFlavor.AbstractAlignment Man page
getFlavor.AromaSeqTransform Man page
getFlavor.Bowtie2Alignment Man page
getFlavor.BwaAlignment Man page
getFlavor.PicardDuplicateRemoval Man page
getFlowcellId Man page
getFlowcellId.IlluminaFastqDataFile Man page
getFullName.AbstractAlignment Man page
getFullName.AromaSeqTransform Man page
getFullName.Bowtie2Alignment Man page
getFullName.BwaAlignment Man page
getFullName.PicardDuplicateRemoval Man page
getGcContent Man page
getGcContent.AromaUnitNucleotideCountsFile Man page
getGcContentFile Man page
getGcContentFile.BinnedGcNormalization Man page
getGeometry Man page
getGeometry.FastqDataFile Man page
getGroupBy Man page
getGroupBy.FileGroupsInterface Man page
getGroupNames Man page
getGroupNames.FileGroupsInterface Man page
getGroups Man page
getGroups.FileGroupsInterface Man page
getHeader.BamDataFile Man page
getHeader.SamDataFile Man page
getIndexFile Man page
getIndexFile.BamDataFile Man page
getIndexFile.FastaReferenceFile Man page
getIndexPrefix Man page
getIndexPrefix.AbstractIndexFile Man page
getIndexPrefix.AbstractIndexSet Man page
getIndexPrefix.Bowtie2IndexFile Man page
getIndexPrefix.BwaIndexFile Man page
getIndexPrefix.BwaIndexSet Man page
getIndexSet Man page
getIndexSet.AbstractAlignment Man page
getIndexSet.Bowtie2Alignment Man page
getIndexSet.BwaAlignment Man page
getIndexStats Man page
getIndexStats.BamDataFile Man page
getInputDataSet Man page
getInputDataSet.AbstractAlignment Man page
getInputDataSet.AromaSeqTransform Man page
getInputDataSet.Bowtie2Alignment Man page
getInputDataSet.BwaAlignment Man page
getInputDataSet.FastqDownsampler Man page
getInputDataSet.FileGroupsInterface Man page
getInputDataSet.PicardDuplicateRemoval Man page
getInstrumentId Man page
getInstrumentId.IlluminaFastqDataFile Man page
getKnownOrganisms Man page
getKnownOrganisms.AromaSeq Man page
getLane Man page
getLane.IlluminaFastqDataFile Man page
getMateFile Man page
getMateFile.FastqDataFile Man page
getName.AbstractAlignment Man page
getName.AromaSeqTransform Man page
getName.Bowtie2Alignment Man page
getName.BwaAlignment Man page
getName.PicardDuplicateRemoval Man page
getOptionalArguments.AbstractAlignment Man page
getOptionalArguments.AromaSeqTransform Man page
getOptionalArguments.Bowtie2Alignment Man page
getOptionalArguments.BwaAlignment Man page
getOptionalArguments.PicardDuplicateRemoval Man page
getOrganism Man page
getOrganism.AbstractAlignment Man page
getOrganism.AbstractIndexSet Man page
getOrganism.Arguments Man page
getOrganism.AromaPathnameInterface Man page
getOrganism.AromaSeqDataFile Man page
getOrganism.AromaSeqDataFileSet Man page
getOrganism.AromaSeqTransform Man page
getOrganism.BamDataSet Man page
getOrganism.FastaReferenceFile Man page
getOrganism.FastaReferenceSet Man page
getOrganism.FastqDataSet Man page
getOrganism.GtfDataFile Man page
getOrganism.HTSeqCountDataSet Man page
getOrganism.SamDataSet Man page
getOrganism.SraDataSet Man page
getOrganismName Man page
getOrganismName.GenericDataFile Man page
getOutputDataSet Man page
getOutputDataSet.AbstractAlignment Man page
getOutputDataSet.AromaSeqTransform Man page
getOutputDataSet.BamDownsampler Man page
getOutputDataSet.BamMerger Man page
getOutputDataSet.Bowtie2Alignment Man page
getOutputDataSet.FastQCReporter Man page
getOutputDataSet.FastqDownsampler Man page
getOutputDataSet.FileGroupsInterface Man page
getOutputDataSet.HTSeqCounting Man page
getOutputDataSet.PicardDuplicateRemoval Man page
getOutputDataSet.QDNAseqEstimation Man page
getOutputDataSet.TopHat2Alignment Man page
getOutputDataSet.TotalCnBinnedCounting Man page
getOutputDataSet0.BinnedGcNormalization Man page
getOutputDataSet0.GatkAlleleCounting Man page
getOutputFileClass Man page
getOutputFileClass.BinnedGcNormalization Man page
getOutputFileExtension Man page
getOutputFileExtension.BinnedGcNormalization Man page
getOutputFileExtension.TotalCnBinnedCounting Man page
getOutputFileSetClass Man page
getOutputFileSetClass.BinnedGcNormalization Man page
getOutputFileSetClass.TotalCnBinnedCounting Man page
getOutputFiles.BinnedGcNormalization Man page
getOutputPath Man page
getOutputPath.FastqDownsampler Man page
getOutputRootPath Man page
getOutputRootPath.FastqDownsampler Man page
getParameterSets.AbstractAlignment Man page
getParameterSets.BwaAlignment Man page
getParameterSets.PicardDuplicateRemoval Man page
getParameters.AromaSeqTransform Man page
getParameters.BinnedGcNormalization Man page
getParameters.Bowtie2Alignment Man page
getParameters.BwaAlignment Man page
getParameters.GatkAlleleCounting Man page
getParameters.HTSeqCounting Man page
getParameters.PicardDuplicateRemoval Man page
getParameters.TopHat2Alignment Man page
getParameters.TopHatAlignment Man page
getPath.AbstractAlignment Man page
getPath.AromaSeqTransform Man page
getPath.BinnedGcNormalization Man page
getPath.Bowtie2Alignment Man page
getPath.BwaAlignment Man page
getPath.FastqDownsampler Man page
getPath.GatkAlleleCounting Man page
getPath.PicardDuplicateRemoval Man page
getPath.TopHat2Alignment Man page
getPlatform.BamDataFile Man page
getPlatform.BamDataSet Man page
getPlatform.IlluminaFastqDataFile Man page
getPlatformUnit Man page
getPlatformUnit.IlluminaFastqDataFile Man page
getProgram Man page
getProgram.BamDataFile Man page
getProgramString Man page
getProgramString.BamDataFile Man page
getPrograms Man page
getPrograms.BamDataFile Man page
getReadCounts Man page
getReadCounts.BamDataFile Man page
getReadDirection Man page
getReadDirection.IlluminaFastqDataFile Man page
getReadGroup Man page
getReadGroup.BamDataFile Man page
getReadGroups Man page
getReadGroups.BamDataFile Man page
getReferenceFile Man page
getReferenceFile.Bowtie2Alignment Man page
getRootPath Man page
getRootPath.AbstractAlignment Man page
getRootPath.AromaSeqTransform Man page
getRootPath.BamDownsampler Man page
getRootPath.BinnedGcNormalization Man page
getRootPath.Bowtie2Alignment Man page
getRootPath.BwaAlignment Man page
getRootPath.FastQCReporter Man page
getRootPath.FastqDownsampler Man page
getRootPath.GatkAlleleCounting Man page
getRootPath.HTSeqCounting Man page
getRootPath.PicardDuplicateRemoval Man page
getRootPath.QDNAseqEstimation Man page
getRootPath.SamTransform Man page
getRootPath.TopHat2Alignment Man page
getSamReadGroup Man page
getSamReadGroup.FastqDataFile Man page
getSamReadGroup.FastqDataSet Man page
getSampleName.FastQCDataFile Man page
getSampleName.GenericDataFile Man page
getSampleName.IlluminaFastqDataFile Man page
getSampleNames.Bowtie2Alignment Man page
getSampleNames.HTSeqCounting Man page
getSampleNames.TopHat2Alignment Man page
getSampleSize Man page
getSampleSize.BamDownsampler Man page
getSampleSize.FastqDownsampler Man page
getSeqGenericSummary Man page
getSeqGenericSummary.SequenceContigsInterface Man page
getSeqLengths Man page
getSeqLengths,BwaIndexSet-method Man page
getSeqLengths.BamDataFile Man page
getSeqLengths.Bowtie2IndexSet Man page
getSeqLengths.BwaIndexSet Man page
getSeqLengths.FastaReferenceFile Man page
getSeqLengths.FastaReferenceIndexFile Man page
getSeqLengths.GcBaseFile Man page
getSeqLengths.GtfDataFile Man page
getSeqLengths.SequenceContigsInterface Man page
getSeqNames Man page
getSeqNames,BwaIndexSet-method Man page
getSeqNames.BamDataFile Man page
getSeqNames.Bowtie2IndexSet Man page
getSeqNames.BwaIndexSet Man page
getSeqNames.FastaReferenceFile Man page
getSeqNames.FastaReferenceIndexFile Man page
getSeqNames.GcBaseFile Man page
getSeqNames.GtfDataFile Man page
getSeqNames.SequenceContigsInterface Man page
getSeqOrdering Man page
getSeqOrdering.SequenceContigsInterface Man page
getSequenceNames Man page
getSequenceNames.Bowtie2IndexSet Man page
getSummary Man page
getSummary.Bowtie2IndexSet Man page
getTags.AbstractAlignment Man page
getTags.AromaSeqTransform Man page
getTags.Bowtie2Alignment Man page
getTags.BwaAlignment Man page
getTags.FastqDownsampler Man page
getTags.PicardDuplicateRemoval Man page
getTargetLengths Man page
getTargetLengths.BamDataFile Man page
getTargetLengths.SamDataFile Man page
getTargetNames Man page
getTargetNames.BamDataFile Man page
getTargetNames.SamDataFile Man page
getTargets Man page
getTargets.BamDataFile Man page
getTargets.SamDataFile Man page
getTotalSeqLength Man page
getTotalSeqLength.SequenceContigsInterface Man page
getTotalSeqLengths Man page
getTotalSeqLengths.FastaReferenceFile Man page
getTotalSeqLengths.FastaReferenceIndexFile Man page
getTotalTargetLength Man page
getTotalTargetLength.BamDataFile Man page
getTotalTargetLength.SamDataFile Man page
getTuxedoOption Man page
getTuxedoOption.Arguments Man page
getTypeOfSeqNames Man page
getTypeOfSeqNames.FastaReferenceFile Man page
hasCommas Man page
hasDescription Man page
hasDescription.SamReadGroup Man page
hasDuplicatedSeqs Man page
hasDuplicatedSeqs.SequenceContigsInterface Man page
hasID Man page
hasID.SamReadGroup Man page
hasIndex Man page
hasIndex.BamDataFile Man page
hasIndex.FastaReferenceFile Man page
hasIndex.SamDataFile Man page
hasLibrary Man page
hasLibrary.SamReadGroup Man page
hasPlatform Man page
hasPlatform.SamReadGroup Man page
hasPlatformUnit Man page
hasPlatformUnit.SamReadGroup Man page
hasRunDate Man page
hasRunDate.SamReadGroup Man page
hasSample Man page
hasSample.SamReadGroup Man page
hasSeqLengths Man page
hasSeqLengths.SequenceContigsInterface Man page
hasSequencingCenter Man page
hasSequencingCenter.SamReadGroup Man page
hasSpaces Man page
htable Man page
htseqCount Man page
htseqCount.default Man page
importFromBSgenome Man page
importFromBSgenome.AromaUnitNucleotideCountsFile Man page
isCapableOf Man page
isCapableOf,AromaSeq-method Man page
isCapableOf.AromaSeq Man page
isCompatibleWith,BwaIndexSet-method Man page
isCompatibleWith.AromaSeqDataFile Man page
isCompatibleWith.AromaSeqDataFileSet Man page
isCompatibleWith.Bowtie2IndexSet Man page
isCompatibleWith.BwaIndexSet Man page
isCompatibleWith.FastaReferenceFile Man page
isCompatibleWith.GcBaseFile Man page
isCompatibleWithBySeqLengths Man page
isCompatibleWithBySeqLengths.SequenceContigsInterface Man page
isCompatibleWithBySeqNames Man page
isCompatibleWithBySeqNames.SequenceContigsInterface Man page
isCompatibleWithBySeqNames.default Man page
isCompatibleWithBySeqs Man page
isCompatibleWithBySeqs.SequenceContigsInterface Man page
isComplete Man page
isComplete,BwaIndexSet-method Man page
isComplete.AbstractIndexSet Man page
isComplete.Bowtie2IndexSet Man page
isComplete.BwaIndexSet Man page
isDone.AromaSeqTransform Man page
isDone.TopHat2Alignment Man page
isEmpty Man page
isEmpty.SamReadGroup Man page
isPaired.AbstractAlignment Man page
isPaired.FastqDataFile Man page
isPaired.FastqDataSet Man page
isSorted Man page
isSorted.BamDataFile Man page
isSorted.SamDataFile Man page
isTopHat2IndexSet Man page
isTopHat2IndexSet.Bowtie2IndexSet Man page
length.AromaSeqTransform Man page
loadCacheFile Man page
loadCacheFile.GenericDataFile Man page
loadCacheFileItem Man page
loadCacheFileItem.GenericDataFile Man page
memoizedCall2 Man page
memoizedCall2.GenericDataFile Man page
merge.SamReadGroup Man page
nbrOfFiles.AbstractAlignment Man page
nbrOfFiles.Bowtie2Alignment Man page
nbrOfFiles.BwaAlignment Man page
nbrOfFiles.PicardDuplicateRemoval Man page
nbrOfGroups Man page
nbrOfGroups.FileGroupsInterface Man page
nbrOfMappedReads Man page
nbrOfMappedReads.BamDataFile Man page
nbrOfReads.BamDataFile Man page
nbrOfSeqs Man page
nbrOfSeqs.BamDataFile Man page
nbrOfSeqs.FastaReferenceFile Man page
nbrOfSeqs.FastaReferenceIndexFile Man page
nbrOfSeqs.FastqDataFile Man page
nbrOfSeqs.SamDataFile Man page
nbrOfSeqs.SequenceContigsInterface Man page
nbrOfTargets Man page
nbrOfTargets.BamDataFile Man page
nbrOfTargets.SamDataFile Man page
nbrOfUnmappedReads Man page
nbrOfUnmappedReads.BamDataFile Man page
normalizeGcContent Man page
normalizeGcContent.default Man page
onExit Man page
pi3 Man page
picardValidateSamFile Man page
picardValidateSamFile.default Man page
process Man page
process,Bowtie2Alignment-method Man page
process,BwaAlignment-method Man page
process.AbstractAlignment Man page
process.AromaSeqTransform Man page
process.BamDownsampler Man page
process.BamMerger Man page
process.BinnedGcNormalization Man page
process.Bowtie2Alignment Man page
process.BwaAlignment Man page
process.FastQCReporter Man page
process.FastqDownsampler Man page
process.GatkAlleleCounting Man page
process.HTSeqCounting Man page
process.PicardDuplicateRemoval Man page
process.QDNAseqEstimation Man page
process.TopHat2Alignment Man page
process.TopHatAlignment Man page
process.TotalCnBinnedCounting Man page
processOne Man page
processOne.Bowtie2Alignment Man page
queryBowtie2 Man page
readAnnData Man page
readAnnData,BwaIndexSet-method Man page
readAnnData.BwaIndexSet Man page
readAnnotationData Man page
readAnnotationData.SeqzFile Man page
readAnnotationData.SeqzFileSet Man page
readDGE Man page
readDGE,HTSeqCountDataSet-method Man page
readDGE.HTSeqCountDataSet Man page
readDataFrame.BamDataFile Man page
readDataFrame.FastaReferenceIndexFile Man page
readDataFrameForPSCBS Man page
readDataFrameForPSCBS.CnvKitCopyNumberRatioFile Man page
readFASTQSummary Man page
readFASTQSummary.FastqDataFile Man page
readGatkCountFile Man page
readGatkCountFile.GatkAlleleCounting Man page
readGeometry Man page
readGeometry.FastqDataFile Man page
readHeader Man page
readHeader.BamDataFile Man page
readHeader.SamDataFile Man page
readReadPositions Man page
readReadPositions.BamDataFile Man page
readSeqFile Man page
readSeqFile.FastqDataFile Man page
readSeqLengths Man page
readSeqLengths,Bowtie2IndexSet-method Man page
readSeqLengths.Bowtie2IndexSet Man page
readSeqLengths.FastaReferenceFile Man page
readSeqLengths.FastaReferenceIndexFile Man page
readTotalCNsAndBAFs Man page
readTotalCNsAndBAFs.SeqzFile Man page
replaceAllReadGroups Man page
replaceAllReadGroups.BamDataFile Man page
report Man page
report.FastqDataFile Man page
report.FastqDataSet Man page
samtoolsFaidx Man page
samtoolsFaidx.default Man page
samtoolsMpileup Man page
samtoolsMpileup.default Man page
samtoolsSort Man page
samtoolsSort.default Man page
samtoolsView Man page
samtoolsView.default Man page
saveCacheFile Man page
saveCacheFile.GenericDataFile Man page
saveCacheFileItem Man page
saveCacheFileItem.GenericDataFile Man page
segmentByCBS.CnvKitCopyNumberRatioFile Man page
setSamReadGroup Man page
setSamReadGroup.FastqDataFile Man page
setSamReadGroup.FastqDataSet Man page
setTags.AbstractAlignment Man page
setTags.AromaSeqTransform Man page
setTags.Bowtie2Alignment Man page
setTags.BwaAlignment Man page
setTags.PicardDuplicateRemoval Man page
setupExampleData Man page
setupTests Man page
setupTests.AromaSeq Man page
skeleton Man page
skeleton.AromaSeq Man page
smoothRawCopyNumbers Man page
smoothRawCopyNumbers.TotalCnBinnedCounting Man page
sort.BamDataFile Man page
sort.SamDataFile Man page
sortByName Man page
sortByName.BamDataFile Man page
sortByName.BamDataSet Man page
sortByPosition Man page
sortByPosition.BamDataFile Man page
sortByPosition.BamDataSet Man page
splitByTargetType Man page
splitByTargetType.BamDataSet Man page
splitUp Man page
splitUp.FastqDataFile Man page
systemBWA Man page
systemBWA.default Man page
systemBowtie2 Man page
systemBowtie2.default Man page
systemBowtie2Build Man page
systemBowtie2Build.default Man page
systemCuffdiff Man page
systemCuffdiff.default Man page
systemCufflinks Man page
systemCufflinks.default Man page
systemFastQC Man page
systemFastQC.default Man page
systemFastqDump Man page
systemFastqDump.default Man page
systemGATK Man page
systemGATK.default Man page
systemGenericCmd Man page
systemGenericCmd.default Man page
systemHTSeqCount Man page
systemHTSeqCount.default Man page
systemJava Man page
systemJava.default Man page
systemJavaJar Man page
systemJavaJar.default Man page
systemPicard Man page
systemPicard.default Man page
systemSamtools Man page
systemSamtools.default Man page
systemSraToolkit Man page
systemSraToolkit.default Man page
systemTopHat Man page
systemTopHat.default Man page
systemTopHatBuild Man page
systemTopHatBuild.default Man page
testSystemBowtie2Build Man page
tophat Man page
tophat.default Man page
tophat1 Man page
tophat1.default Man page
tophat2 Man page
tophat2.default Man page
tview Man page
tview.BamDataFile Man page
typeOfSequenceOrdering Man page
typeOfSequenceOrdering.character Man page
typeOfSequenceOrdering.numeric Man page
updateDirectoryStructure Man page
updateDirectoryStructure.GenericDataFileSet Man page
validate,BamDataFile-method Man page
validate.BamDataFile Man page
validate.BamDataSet Man page
validate.FastaReferenceSet Man page
validate.FastqDataSet Man page
validate.IlluminaFastqDataSet Man page
validate.SamDataFile Man page
validate.SamDataSet Man page
validate.SamReadGroup Man page
validateGroups Man page
validateGroups.BamMerger Man page
validateGroups.Bowtie2Alignment Man page
validateGroups.FastQCReporter Man page
validateGroups.FileGroupsInterface Man page
validateGroups.TopHat2Alignment Man page
writeBedDataFile Man page
writeBedDataFile.AromaUgpFile Man page
writeFastaReferenceFile Man page
writeFastaReferenceFile,FastaReferenceSet-method Man page
writeFastaReferenceFile.FastaReferenceSet Man page
writeSample Man page
writeSample.BamDataFile Man page
writeSample.FastqDataFile Man page
HenrikBengtsson/aroma.seq documentation built on June 13, 2019, 10:20 a.m.