| .onAttach |
Source code
|
| .onLoad |
Source code
|
| .optionsList2String |
Source code
|
| .stop_if_not |
Source code
|
| 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
|
| `directoryStructure<-` |
Source code
|
| agsub |
Man page
Source code
|
| 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
Source code
|
| assertNoDuplicated |
Man page
Source code
|
| assertNoSpaces |
Man page
Source code
|
| assignBy |
Man page
|
| assignBy.SamReadGroup |
Man page
|
| bDebugSystemBowtie2Build |
Man page
|
| binTabulate |
Man page
|
| binTabulate.MaskedDNAString |
Man page
|
| bowtie2 |
Man page
Source code
|
| 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
Source code
|
| findBowtie2 |
Man page
Source code
|
| 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
Source code
|
| findCmd |
Man page
|
| findCmd.default |
Man page
|
| findCmdv |
Man page
|
| findCmdv.default |
Man page
|
| findExternal |
Man page
Source code
|
| findFastQC |
Man page
Source code
|
| findFastqDump |
Man page
Source code
|
| findFilesTodo |
Man page
|
| findFilesTodo.AromaSeqTransform |
Man page
|
| findFilesTodo.TotalCnBinnedCounting |
Man page
|
| findGATK |
Man page
Source code
|
| findHTSeq |
Man page
Source code
|
| findJava |
Man page
Source code
|
| findMateFile |
Man page
|
| findMateFile.FastqDataFile |
Man page
|
| findPerl |
Man page
Source code
|
| findPicard |
Man page
Source code
|
| findPython |
Man page
Source code
|
| findRspReportTemplate |
Man page
|
| findRspReportTemplate.FastqDataFile |
Man page
|
| findRspReportTemplate.FastqDataSet |
Man page
|
| findRspReportTemplate.Object |
Man page
|
| findSamtools |
Man page
Source code
|
| findSraToolkit |
Man page
Source code
|
| findTopHat |
Man page
Source code
|
| findTopHat1 |
Man page
Source code
|
| findTopHat2 |
Man page
Source code
|
| 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
Source code
|
| 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
Source code
|
| 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
Source code
|
| htable |
Man page
Source code
|
| 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
Source code
|
| pi3 |
Man page
Source code
|
| picardValidateSamFile |
Man page
|
| picardValidateSamFile.default |
Man page
|
| pileup2seqz |
Source code
|
| 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
Source code
|
| 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
Source code
|
| 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
|
