| !,SRFilterResult-method |
Man page
|
| %in%,AlignedRead,IntegerRangesList-method |
Man page
|
| .AlignedRead_QualityConstructor |
Source code
|
| .AlignedRead_subset |
Source code
|
| .AlignedRead_validity |
Source code
|
| .BowtieQA |
Source code
|
| .Bowtie_AlignedDataFrame |
Source code
|
| .FastqQA |
Source code
|
| .FastqQuality_abc |
Source code
|
| .FastqQuality_af |
Source code
|
| .FastqQuality_ascore |
Source code
|
| .FastqQuality_character |
Source code
|
| .FastqQuality_missing |
Source code
|
| .FastqQuality_srduplicated |
Source code
|
| .MAQMapQA |
Source code
|
| .MatrixQuality_subset |
Source code
|
| .MatrixQuality_subset2 |
Source code
|
| .QA-class |
Man page
|
| .QA2-class |
Man page
|
| .QASummaryFactory |
Source code
|
| .QualityScore_subset |
Source code
|
| .QualityScore_subset2 |
Source code
|
| .Roche-class |
Man page
|
| .RocheSet_RochePath |
Source code
|
| .SFastqQuality_ascore |
Source code
|
| .SOAP_AlignedDataFrame |
Source code
|
| .SRList_show_class |
Source code
|
| .SRSet_validity |
Source code
|
| .SRUtil-class |
Man page
|
| .ShortReadBase-class |
Man page
|
| .ShortReadQQA |
Source code
|
| .ShortReadQ_subset |
Source code
|
| .ShortRead_subset |
Source code
|
| .ShortRead_validity |
Source code
|
| .Solexa-class |
Man page
|
| .SolexaExportQA |
Source code
|
| .SolexaExport_AlignedDataFrame |
Source code
|
| .SolexaRealignQA |
Source code
|
| .SolexaSet_SolexaPath |
Source code
|
| .abc_BStringSet |
Source code
|
| .abc_ShortRead |
Source code
|
| .abc_ShortReadQ |
Source code
|
| .append.factor |
Source code
|
| .arg_mismatch_type_err |
Source code
|
| .arg_mismatch_type_err2 |
Source code
|
| .arg_mismatch_value_err |
Source code
|
| .arg_missing_err |
Source code
|
| .atQuantile |
Source code
|
| .binReader |
Source code
|
| .bind |
Source code
|
| .checkClass |
Source code
|
| .checkPath |
Source code
|
| .check_type_and_length |
Source code
|
| .coarse_annviewer |
Source code
|
| .coarse_coverage_reader |
Source code
|
| .colorkeyNames |
Source code
|
| .coverage_as_dataframe |
Source code
|
| .coverage_viewer |
Source code
|
| .currentFunction |
Source code
|
| .detail_additionalPathSlots |
Source code
|
| .df2a |
Source code
|
| .file_names |
Source code
|
| .filter1 |
Source code
|
| .filterFastq_check_fnames |
Source code
|
| .filterUpdate |
Source code
|
| .fine_annviewer |
Source code
|
| .fine_coverage_reader |
Source code
|
| .forward_obj |
Source code
|
| .forward_objq |
Source code
|
| .forward_x |
Source code
|
| .forward_xq |
Source code
|
| .freqSequences |
Source code
|
| .getAlphabetFrequency |
Source code
|
| .getData |
Source code
|
| .get_coarse_coverage |
Source code
|
| .get_fine_coverage |
Source code
|
| .htmlReadOccur |
Source code
|
| .htmlReadQuality |
Source code
|
| .html_NA |
Source code
|
| .html_img |
Source code
|
| .hwrite |
Source code
|
| .make_getter |
Source code
|
| .maq_reverse |
Source code
|
| .maqmap_file_list_error |
Source code
|
| .multiFile_coverage_as_dataframe |
Source code
|
| .multicoarse_coverage_reader |
Source code
|
| .multicoverage_viewer |
Source code
|
| .multifine_coverage_reader |
Source code
|
| .nameAll |
Source code
|
| .occurrenceName |
Source code
|
| .plotAlignQuality |
Source code
|
| .plotCycleBaseCall |
Source code
|
| .plotCycleQuality |
Source code
|
| .plotDepthOfCoverage |
Source code
|
| .plotMultipleAlignmentCount |
Source code
|
| .plotNucleotideCount |
Source code
|
| .plotReadCount |
Source code
|
| .plotReadOccurrences |
Source code
|
| .plotReadQuality |
Source code
|
| .plotTileCounts |
Source code
|
| .plotTileLocalCoords |
Source code
|
| .plotTileQualityScore |
Source code
|
| .ppnCount |
Source code
|
| .qa2_do_collate1 |
Source code
|
| .qa_Bowtie |
Source code
|
| .qa_Bowtie_lane |
Source code
|
| .qa_MAQMap |
Source code
|
| .qa_MAQMap_lane |
Source code
|
| .qa_ShortReadQ |
Source code
|
| .qa_SolexaExport |
Source code
|
| .qa_SolexaExport_lane |
Source code
|
| .qa_SolexaPath |
Source code
|
| .qa_SolexaRealign |
Source code
|
| .qa_SolexaRealign_lane |
Source code
|
| .qa_Solexa_tileStats |
Source code
|
| .qa_adapterContamination |
Source code
|
| .qa_alphabetFrequency |
Source code
|
| .qa_character |
Source code
|
| .qa_depthOfCoverage |
Source code
|
| .qa_fastq |
Source code
|
| .qa_fastq_lane |
Source code
|
| .qa_lst_as_data_frame |
Source code
|
| .qa_perCycleBaseCall |
Source code
|
| .qa_perCycleQuality |
Source code
|
| .qa_qdensity |
Source code
|
| .qa_sampleKey |
Source code
|
| .qualityTypeAuto |
Source code
|
| .readAligned_Bowtie |
Source code
|
| .readAligned_MaqMap |
Source code
|
| .readAligned_MaqMapOld |
Source code
|
| .readAligned_MaqMapview |
Source code
|
| .readAligned_Maq_ADF |
Source code
|
| .readAligned_SOAP |
Source code
|
| .readAligned_SolexaAlign |
Source code
|
| .readAligned_SolexaExport |
Source code
|
| .readAligned_SolexaPath |
Source code
|
| .readAligned_SolexaResult |
Source code
|
| .readAligned_SolexaSet |
Source code
|
| .readAligned_character |
Source code
|
| .readBaseQuality_Solexa |
Source code
|
| .readBaseQuality_SolexaPath |
Source code
|
| .readBaseQuality_character |
Source code
|
| .readFastaQual_RochePath |
Source code
|
| .readFastaQual_character |
Source code
|
| .readFasta_RochePath |
Source code
|
| .readFastq_SolexaPath |
Source code
|
| .readIntensities_IparIntensity |
Source code
|
| .readIntensities_RtaIntensity |
Source code
|
| .readIntensities_SolexaIntensity |
Source code
|
| .readIntensities_SolexaPath |
Source code
|
| .readIntensities_character |
Source code
|
| .readPrb |
Source code
|
| .readPrb_IntegerEncoding |
Source code
|
| .readPrb_SolexaPath |
Source code
|
| .readPrb_array |
Source code
|
| .readPrb_character |
Source code
|
| .readPrb_quality |
Source code
|
| .readQseq_DataFrame |
Source code
|
| .readQseq_ShortReadQ |
Source code
|
| .readQseq_character |
Source code
|
| .readQual |
Source code
|
| .readQual_RochePath |
Source code
|
| .read_cif_or_cnf |
Source code
|
| .read_cif_or_cnf_file |
Source code
|
| .read_csv_portion |
Source code
|
| .read_ipar_int_array |
Source code
|
| .renewable_of |
Source code
|
| .renewable_query |
Source code
|
| .report_html_do |
Source code
|
| .report_pdf_do |
Source code
|
| .runNames_RochePath |
Source code
|
| .sampleNames_RochePath |
Source code
|
| .show_KoverA |
Source code
|
| .show_additionalPathSlots |
Source code
|
| .show_some |
Source code
|
| .srPath |
Source code
|
| .srValidity |
Source code
|
| .srdistance |
Source code
|
| .srdistanceDNA |
Source code
|
| .srdistance_DNAStringSet_DNAString |
Source code
|
| .srdistance_DNAStringSet_DNAStringSet |
Source code
|
| .srdistance_DNAStringSet_character |
Source code
|
| .srdistance_ShortRead_ANY |
Source code
|
| .stringset_tables |
Source code
|
| .subset_err |
Source code
|
| .tileGeometry |
Source code
|
| .toStrand_Solexa |
Source code
|
| .undefined_method_err |
Source code
|
| .update_viewer |
Source code
|
| AlignedDataFrame |
Man page
Source code
|
| AlignedDataFrame-class |
Man page
|
| AlignedRead |
Man page
Source code
|
| AlignedRead-class |
Man page
|
| ArrayIntensity |
Man page
Source code
|
| ArrayIntensity-class |
Man page
|
| BowtieQA-class |
Man page
|
| ExperimentPath |
Man page
Source code
|
| ExperimentPath-class |
Man page
|
| FastqFile |
Man page
Source code
|
| FastqFile-class |
Man page
|
| FastqFileList |
Man page
|
| FastqFileList,ANY-method |
Man page
|
| FastqFileList,character-method |
Man page
|
| FastqFileList-class |
Man page
|
| FastqFileReader-class |
Man page
|
| FastqQA |
Man page
|
| FastqQA-class |
Man page
|
| FastqQuality |
Man page
|
| FastqQuality,BStringSet-method |
Man page
|
| FastqQuality,character-method |
Man page
|
| FastqQuality,missing-method |
Man page
|
| FastqQuality-class |
Man page
|
| FastqSampler |
Man page
Source code
|
| FastqSampler-class |
Man page
|
| FastqSamplerList |
Man page
|
| FastqSamplerList,ANY-method |
Man page
|
| FastqSamplerList,character-method |
Man page
|
| FastqSamplerList-class |
Man page
|
| FastqStreamer |
Man page
|
| FastqStreamer,ANY,IRanges-method |
Man page
|
| FastqStreamer,ANY,missing-method |
Man page
|
| FastqStreamer,ANY,numeric-method |
Man page
|
| FastqStreamer-class |
Man page
|
| FastqStreamerList |
Man page
|
| FastqStreamerList,ANY-method |
Man page
|
| FastqStreamerList,character-method |
Man page
|
| FastqStreamerList-class |
Man page
|
| IntegerQuality |
Man page
Source code
|
| IntegerQuality-class |
Man page
|
| Intensity-class |
Man page
|
| IntensityInfo-class |
Man page
|
| IntensityMeasure-class |
Man page
|
| Logic,SRFilterResult,SRFilterResult-method |
Man page
|
| MAQMapQA |
Man page
|
| MAQMapQA-class |
Man page
|
| MatrixQuality |
Man page
Source code
|
| MatrixQuality-class |
Man page
|
| NumericQuality |
Man page
Source code
|
| NumericQuality-class |
Man page
|
| QA |
Man page
|
| QA-class |
Man page
Man page
|
| QAAdapterContamination |
Man page
|
| QAAdapterContamination-class |
Man page
|
| QACollate |
Man page
|
| QACollate,QAFastqSource-method |
Man page
|
| QACollate,missing-method |
Man page
|
| QACollate-class |
Man page
|
| QAData |
Man page
Source code
|
| QAData-class |
Man page
|
| QAFastqSource |
Man page
Source code
|
| QAFastqSource-class |
Man page
|
| QAFiltered |
Man page
|
| QAFiltered-class |
Man page
|
| QAFlagged |
Man page
|
| QAFlagged-class |
Man page
|
| QAFrequentSequence |
Man page
|
| QAFrequentSequence-class |
Man page
|
| QANucleotideByCycle |
Man page
|
| QANucleotideByCycle-class |
Man page
|
| QANucleotideUse |
Man page
|
| QANucleotideUse-class |
Man page
|
| QAQualityByCycle |
Man page
|
| QAQualityByCycle-class |
Man page
|
| QAQualityUse |
Man page
|
| QAQualityUse-class |
Man page
|
| QAReadQuality |
Man page
Source code
|
| QAReadQuality-class |
Man page
|
| QASequenceUse |
Man page
|
| QASequenceUse-class |
Man page
|
| QASource-class |
Man page
|
| QASummary-class |
Man page
|
| QualityScore-class |
Man page
|
| RochePath |
Man page
Source code
|
| RochePath-class |
Man page
|
| RocheSet |
Man page
|
| RocheSet,RochePath-method |
Man page
|
| RocheSet,character-method |
Man page
|
| RocheSet-class |
Man page
|
| RtaIntensity |
Man page
Source code
|
| RtaIntensity-class |
Man page
|
| SFastqQuality |
Man page
|
| SFastqQuality,BStringSet-method |
Man page
|
| SFastqQuality,character-method |
Man page
|
| SFastqQuality,missing-method |
Man page
|
| SFastqQuality-class |
Man page
|
| SRError |
Man page
Source code
|
| SRError-class |
Man page
|
| SRFilter-class |
Man page
|
| SRFilterResult |
Man page
Source code
|
| SRFilterResult-class |
Man page
|
| SRList |
Man page
Source code
|
| SRList-class |
Man page
|
| SRSet-class |
Man page
|
| SRVector |
Man page
Source code
|
| SRVector-class |
Man page
|
| SRWarn |
Man page
Source code
|
| SRWarn-class |
Man page
|
| ShortRead |
Man page
|
| ShortRead,DNAStringSet,BStringSet-method |
Man page
|
| ShortRead,DNAStringSet,missing-method |
Man page
|
| ShortRead,missing,missing-method |
Man page
|
| ShortRead-class |
Man page
|
| ShortReadBase-package |
Man page
|
| ShortReadFile-class |
Man page
|
| ShortReadQ |
Man page
|
| ShortReadQ,DNAStringSet,BStringSet,BStringSet-method |
Man page
|
| ShortReadQ,DNAStringSet,BStringSet,missing-method |
Man page
|
| ShortReadQ,DNAStringSet,QualityScore,BStringSet-method |
Man page
|
| ShortReadQ,DNAStringSet,QualityScore,missing-method |
Man page
|
| ShortReadQ,missing,missing,missing-method |
Man page
|
| ShortReadQ-class |
Man page
|
| ShortReadQQA-class |
Man page
|
| Snapshot |
Man page
|
| Snapshot,BamFileList,GRanges-method |
Man page
|
| Snapshot,character,GRanges-method |
Man page
|
| Snapshot,character,missing-method |
Man page
|
| Snapshot-class |
Man page
|
| SnapshotFunction |
Man page
Source code
|
| SnapshotFunction-class |
Man page
|
| SnapshotFunctionList |
Man page
|
| SnapshotFunctionList,ANY-method |
Man page
|
| SnapshotFunctionList,SnapshotFunction-method |
Man page
|
| SnapshotFunctionList-class |
Man page
|
| SolexaExportQA |
Man page
|
| SolexaExportQA-class |
Man page
|
| SolexaIntensity |
Man page
Source code
|
| SolexaIntensity-class |
Man page
|
| SolexaIntensityInfo |
Man page
Source code
|
| SolexaIntensityInfo-class |
Man page
|
| SolexaPath |
Man page
Source code
|
| SolexaPath-class |
Man page
|
| SolexaRealignQA-class |
Man page
|
| SolexaSet |
Man page
|
| SolexaSet,SolexaPath-method |
Man page
|
| SolexaSet,character-method |
Man page
|
| SolexaSet-class |
Man page
|
| SpTrellis |
Man page
Source code
|
| SpTrellis-class |
Man page
|
| [,AlignedRead,ANY,ANY,ANY-method |
Man page
|
| [,AlignedRead,ANY,ANY-method |
Man page
|
| [,AlignedRead,ANY,missing,ANY-method |
Man page
|
| [,AlignedRead,ANY,missing-method |
Man page
|
| [,AlignedRead,missing,ANY,ANY-method |
Man page
|
| [,AlignedRead,missing,ANY-method |
Man page
|
| [,AlignedRead,missing,missing,ANY-method |
Man page
|
| [,AlignedRead,missing,missing-method |
Man page
|
| [,IntensityMeasure,ANY,ANY,ANY-method |
Man page
|
| [,IntensityMeasure,ANY,ANY-method |
Man page
|
| [,IntensityMeasure,ANY,missing,ANY-method |
Man page
|
| [,IntensityMeasure,missing,ANY,ANY-method |
Man page
|
| [,IntensityMeasure,missing,missing,ANY-method |
Man page
|
| [,MatrixQuality,ANY,missing,ANY-method |
Man page
|
| [,MatrixQuality,ANY,missing-method |
Man page
|
| [,QualityScore,ANY,missing,ANY-method |
Man page
|
| [,QualityScore,ANY,missing-method |
Man page
|
| [,SRList,ANY,missing,ANY-method |
Man page
|
| [,SRList,ANY,missing-method |
Man page
|
| [,ShortRead,ANY,ANY,ANY-method |
Man page
|
| [,ShortRead,ANY,ANY-method |
Man page
|
| [,ShortRead,ANY,missing,ANY-method |
Man page
|
| [,ShortRead,ANY,missing-method |
Man page
|
| [,ShortRead,missing,ANY,ANY-method |
Man page
|
| [,ShortRead,missing,ANY-method |
Man page
|
| [,ShortRead,missing,missing,ANY-method |
Man page
|
| [,ShortRead,missing,missing-method |
Man page
|
| [,ShortReadQ,ANY,ANY,ANY-method |
Man page
|
| [,ShortReadQ,ANY,ANY-method |
Man page
|
| [,ShortReadQ,ANY,missing,ANY-method |
Man page
|
| [,ShortReadQ,ANY,missing-method |
Man page
|
| [,ShortReadQ,missing,ANY,ANY-method |
Man page
|
| [,ShortReadQ,missing,ANY-method |
Man page
|
| [,ShortReadQ,missing,missing,ANY-method |
Man page
|
| [,ShortReadQ,missing,missing-method |
Man page
|
| [,SolexaIntensity,ANY,ANY,ANY-method |
Man page
|
| [,SolexaIntensity,ANY,ANY-method |
Man page
|
| [,SolexaIntensity,ANY,missing,ANY-method |
Man page
|
| [,SolexaIntensity,missing,ANY,ANY-method |
Man page
|
| [,SolexaIntensity,missing,missing,ANY-method |
Man page
|
| [<-,ShortReadQ,ANY,missing,ShortReadQ-method |
Man page
|
| [[,ArrayIntensity,ANY,ANY-method |
Man page
|
| [[,MatrixQuality,ANY,missing-method |
Man page
|
| [[,QualityScore,ANY,missing-method |
Man page
|
| [[,SRList,ANY,missing-method |
Man page
|
| accessors |
Man page
|
| alignData |
Man page
|
| alignDataFilter |
Man page
Source code
|
| alignQuality |
Man page
|
| alignQualityFilter |
Man page
Source code
|
| alphabet,FastqQuality-method |
Man page
|
| alphabetByCycle |
Man page
Source code
|
| alphabetByCycle,BStringSet-method |
Man page
|
| alphabetByCycle,FastqQuality-method |
Man page
|
| alphabetByCycle,ShortRead-method |
Man page
|
| alphabetByCycle,ShortReadQ-method |
Man page
|
| alphabetFrequency,FastqQuality-method |
Man page
|
| alphabetScore |
Man page
|
| alphabetScore,FastqQuality-method |
Man page
|
| alphabetScore,PhredQuality-method |
Man page
|
| alphabetScore,SFastqQuality-method |
Man page
|
| alphabetScore,ShortReadQ-method |
Man page
|
| analysisPath |
Man page
|
| annTrack |
Man page
|
| annTrack,Snapshot-method |
Man page
|
| append,.ShortReadBase,.ShortReadBase-method |
Man page
|
| append,AlignedDataFrame,AlignedDataFrame-method |
Man page
|
| append,AlignedRead,AlignedRead-method |
Man page
|
| append,MatrixQuality,MatrixQuality-method |
Man page
|
| append,QualityScore,QualityScore-method |
Man page
|
| append,ShortRead,ShortRead-method |
Man page
|
| append,ShortReadQ,ShortReadQ-method |
Man page
|
| baseCallPath |
Man page
|
| basePath |
Man page
Source code
|
| c,SRFilter-method |
Man page
|
| chromosome |
Man page
|
| chromosome,AlignedRead-method |
Man page
|
| chromosomeFilter |
Man page
Source code
|
| clean |
Man page
|
| clean,DNAStringSet-method |
Man page
|
| clean,ShortRead-method |
Man page
|
| close.ShortReadFile |
Man page
Source code
|
| coerce,AlignedRead,GAlignments-method |
Man page
|
| coerce,AlignedRead,GRanges-method |
Man page
|
| coerce,AlignedRead,GappedReads-method |
Man page
|
| coerce,AlignedRead,IntegerRangesList-method |
Man page
|
| coerce,FastqQuality,PhredQuality-method |
Man page
|
| coerce,FastqQuality,matrix-method |
Man page
|
| coerce,FastqQuality,numeric-method |
Man page
|
| coerce,PairwiseAlignments,AlignedRead-method |
Man page
|
| coerce,SFastqQuality,SolexaQuality-method |
Man page
|
| coerce,SFastqQuality,matrix-method |
Man page
|
| coerce,SRFilter,FilterRules-method |
Man page
|
| coerce,ShortReadQ,QualityScaledDNAStringSet-method |
Man page
|
| compose |
Man page
Source code
|
| countFastq |
Man page
|
| countFastq,FastqFile-method |
Man page
|
| countFastq,character-method |
Man page
|
| countLines |
Man page
Source code
|
| coverage,AlignedRead-method |
Man page
|
| dataPath |
Man page
|
| defunct |
Man page
|
| deprecated |
Man page
|
| detail,.ShortReadBase-method |
Man page
|
| detail,AlignedRead-method |
Man page
|
| detail,ExperimentPath-method |
Man page
|
| detail,QualityScore-method |
Man page
|
| detail,RochePath-method |
Man page
|
| detail,SRList-method |
Man page
|
| detail,SRSet-method |
Man page
|
| detail,SRVector-method |
Man page
|
| detail,ShortRead-method |
Man page
|
| detail,ShortReadQ-method |
Man page
|
| detail,SolexaPath-method |
Man page
|
| detail,SolexaSet-method |
Man page
|
| dim,Intensity-method |
Man page
|
| dim,MatrixQuality-method |
Man page
|
| dustyFilter |
Man page
Source code
|
| dustyScore |
Man page
|
| dustyScore,DNAStringSet-method |
Man page
|
| dustyScore,ShortRead-method |
Man page
|
| encoding,FastqQuality-method |
Man page
|
| encoding,SFastqQuality-method |
Man page
|
| experimentPath |
Man page
Source code
|
| experimentPath,SRSet-method |
Man page
|
| fac |
Man page
|
| fac,Snapshot-method |
Man page
|
| files |
Man page
|
| files,Snapshot-method |
Man page
|
| filterFastq |
Man page
Source code
|
| flag |
Man page
|
| flag,.QA2-method |
Man page
|
| flag,QAFrequentSequence-method |
Man page
|
| flag,QAReadQuality-method |
Man page
|
| flag,QASource-method |
Man page
|
| functions |
Man page
|
| functions,Snapshot-method |
Man page
|
| getTrellis |
Man page
|
| getTrellis,Snapshot-method |
Man page
|
| id |
Man page
|
| id,ShortRead-method |
Man page
|
| idFilter |
Man page
Source code
|
| ignore.strand |
Man page
|
| ignore.strand,Snapshot-method |
Man page
|
| imageAnalysisPath |
Man page
|
| intensity |
Man page
|
| laneDescription |
Man page
|
| laneNames |
Man page
|
| laneNames,AnnotatedDataFrame-method |
Man page
|
| laneNames,SolexaSet-method |
Man page
|
| lapply,SRList,ANY-method |
Man page
|
| lapply,SRList-method |
Man page
|
| left |
Man page
|
| left,SpTrellis-method |
Man page
|
| length,MatrixQuality-method |
Man page
|
| length,QualityScore-method |
Man page
|
| length,SRList-method |
Man page
|
| length,ShortRead-method |
Man page
|
| limits |
Man page
Source code
|
| measurementError |
Man page
Source code
|
| nFilter |
Man page
Source code
|
| name |
Man page
|
| name,SRFilter-method |
Man page
|
| name,SRFilterResult-method |
Man page
|
| names,SRList-method |
Man page
|
| names<-,SRList,character-method |
Man page
|
| narrow,FastqQuality-method |
Man page
|
| narrow,MatrixQuality-method |
Man page
|
| narrow,ShortRead-method |
Man page
|
| narrow,ShortReadQ-method |
Man page
|
| occurrenceFilter |
Man page
Source code
|
| open.ShortReadFile |
Man page
Source code
|
| pan |
Man page
|
| pan,Snapshot-method |
Man page
|
| phenoData,SRSet-method |
Man page
|
| polyn |
Man page
Source code
|
| polynFilter |
Man page
Source code
|
| position |
Man page
|
| position,AlignedRead-method |
Man page
|
| positionFilter |
Man page
Source code
|
| qa |
Man page
|
| qa,ShortReadQ-method |
Man page
|
| qa,SolexaPath-method |
Man page
|
| qa,character-method |
Man page
|
| qa,list-method |
Man page
|
| qa2 |
Man page
|
| qa2,FastqSampler-method |
Man page
|
| qa2,QAAdapterContamination-method |
Man page
|
| qa2,QACollate-method |
Man page
|
| qa2,QAFastqSource-method |
Man page
|
| qa2,QAFrequentSequence-method |
Man page
|
| qa2,QANucleotideByCycle-method |
Man page
|
| qa2,QANucleotideUse-method |
Man page
|
| qa2,QAQualityByCycle-method |
Man page
|
| qa2,QAQualityUse-method |
Man page
|
| qa2,QAReadQuality-method |
Man page
|
| qa2,QASequenceUse-method |
Man page
|
| qualPath |
Man page
|
| rbind,.QA-method |
Man page
|
| rbind,QASummary-method |
Man page
|
| read454 |
Man page
|
| read454,RochePath-method |
Man page
|
| readAligned |
Man page
|
| readAligned,BamFile-method |
Man page
|
| readAligned,SolexaPath-method |
Man page
|
| readAligned,SolexaSet-method |
Man page
|
| readAligned,character-method |
Man page
|
| readBaseQuality |
Man page
|
| readBaseQuality,RochePath-method |
Man page
|
| readBaseQuality,SolexaPath-method |
Man page
|
| readBaseQuality,character-method |
Man page
|
| readBfaToc |
Man page
Source code
|
| readCount |
Man page
|
| readData |
Man page
|
| readFasta |
Man page
|
| readFasta,RochePath-method |
Man page
|
| readFasta,SolexaPath-method |
Man page
|
| readFasta,character-method |
Man page
|
| readFastaQual |
Man page
|
| readFastaQual,RochePath-method |
Man page
|
| readFastaQual,character-method |
Man page
|
| readFastq |
Man page
|
| readFastq,FastqFile-method |
Man page
|
| readFastq,SolexaPath-method |
Man page
|
| readFastq,character-method |
Man page
|
| readIndex |
Man page
|
| readIntensities |
Man page
|
| readIntensities,SolexaPath-method |
Man page
|
| readIntensities,character-method |
Man page
|
| readIntensityInfo |
Man page
Source code
|
| readPath |
Man page
|
| readPrb |
Man page
|
| readPrb,SolexaPath-method |
Man page
|
| readPrb,character-method |
Man page
|
| readQseq |
Man page
|
| readQseq,SolexaPath-method |
Man page
|
| readQseq,character-method |
Man page
|
| readQual |
Man page
|
| readQual,RochePath-method |
Man page
|
| readQual,character-method |
Man page
|
| readXStringColumns |
Man page
Source code
|
| reader |
Man page
Source code
|
| renew |
Man page
|
| renew,.ShortReadBase-method |
Man page
|
| renewable |
Man page
|
| renewable,.ShortReadBase-method |
Man page
|
| renewable,character-method |
Man page
|
| renewable,missing-method |
Man page
|
| report |
Man page
|
| report,ANY-method |
Man page
|
| report,BowtieQA-method |
Man page
|
| report,FastqQA-method |
Man page
|
| report,MAQMapQA-method |
Man page
|
| report,QA-method |
Man page
|
| report,QAAdapterContamination-method |
Man page
|
| report,QAFiltered-method |
Man page
|
| report,QAFlagged-method |
Man page
|
| report,QAFrequentSequence-method |
Man page
|
| report,QANucleotideByCycle-method |
Man page
|
| report,QANucleotideUse-method |
Man page
|
| report,QAQualityByCycle-method |
Man page
|
| report,QAQualityUse-method |
Man page
|
| report,QAReadQuality-method |
Man page
|
| report,QASequenceUse-method |
Man page
|
| report,QASource-method |
Man page
|
| report,SolexaExportQA-method |
Man page
|
| report,SolexaPath-method |
Man page
|
| report_html |
Man page
|
| report_html,BowtieQA-method |
Man page
|
| report_html,FastqQA-method |
Man page
|
| report_html,MAQMapQA-method |
Man page
|
| report_html,ShortReadQQA-method |
Man page
|
| report_html,SolexaExportQA-method |
Man page
|
| report_html,SolexaRealignQA-method |
Man page
|
| restore |
Man page
|
| restore,SpTrellis-method |
Man page
|
| reverse,FastqQuality-method |
Man page
|
| reverse,ShortReadQ-method |
Man page
|
| reverseComplement,ShortReadQ-method |
Man page
|
| right |
Man page
|
| right,SpTrellis-method |
Man page
|
| runNames |
Man page
|
| runNames,RochePath-method |
Man page
Man page
|
| sapply,SRList-method |
Man page
|
| scanPath |
Man page
|
| show,.QA-method |
Man page
|
| show,.ShortReadBase-method |
Man page
|
| show,AlignedRead-method |
Man page
|
| show,ExperimentPath-method |
Man page
|
| show,FastqQuality-method |
Man page
|
| show,Intensity-method |
Man page
|
| show,IntensityMeasure-method |
Man page
|
| show,NumericQuality-method |
Man page
|
| show,QAAdapterContamination-method |
Man page
|
| show,QACollate-method |
Man page
|
| show,QAFastqSource-method |
Man page
|
| show,QAFrequentSequence-method |
Man page
|
| show,QAReadQuality-method |
Man page
|
| show,QASummary-method |
Man page
|
| show,RochePath-method |
Man page
|
| show,SRFilter-method |
Man page
|
| show,SRFilterResult-method |
Man page
|
| show,SRList-method |
Man page
|
| show,SRSet-method |
Man page
|
| show,SRVector-method |
Man page
|
| show,ShortRead-method |
Man page
|
| show,Snapshot-method |
Man page
|
| show,SnapshotFunction-method |
Man page
|
| show,SolexaExportQA-method |
Man page
|
| show,SolexaPath-method |
Man page
|
| show,SolexaSet-method |
Man page
|
| show,SpTrellis-method |
Man page
|
| solexaPath |
Man page
|
| sourcePath |
Man page
|
| spViewPerFeature |
Man page
Source code
|
| srFilter |
Man page
|
| srFilter,SRFilter-method |
Man page
|
| srFilter,function-method |
Man page
|
| srFilter,missing-method |
Man page
|
| srapply |
Man page
|
| srdistance |
Man page
|
| srdistance,DNAStringSet,DNAString-method |
Man page
|
| srdistance,DNAStringSet,DNAStringSet-method |
Man page
|
| srdistance,DNAStringSet,character-method |
Man page
|
| srdistance,ShortRead,ANY-method |
Man page
|
| srdistanceFilter |
Man page
Source code
|
| srduplicated |
Man page
|
| srduplicated,AlignedRead-method |
Man page
|
| srduplicated,FastqQuality-method |
Man page
|
| srduplicated,ShortRead-method |
Man page
|
| srduplicated,XStringSet-method |
Man page
|
| sread |
Man page
|
| sread,ShortRead-method |
Man page
|
| srlist |
Man page
|
| srorder |
Man page
|
| srorder,AlignedRead-method |
Man page
|
| srorder,FastqQuality-method |
Man page
|
| srorder,ShortRead-method |
Man page
|
| srorder,XStringSet-method |
Man page
|
| srrank |
Man page
|
| srrank,AlignedRead-method |
Man page
|
| srrank,FastqQuality-method |
Man page
|
| srrank,ShortRead-method |
Man page
|
| srrank,XStringSet-method |
Man page
|
| srsort |
Man page
|
| srsort,FastqQuality-method |
Man page
|
| srsort,ShortRead-method |
Man page
|
| srsort,XStringSet-method |
Man page
|
| stats |
Man page
|
| stats,SRFilterResult-method |
Man page
|
| strand,AlignedRead-method |
Man page
|
| strandFilter |
Man page
Source code
|
| tables |
Man page
|
| tables,ShortRead-method |
Man page
|
| tables,XStringSet-method |
Man page
|
| togglefun |
Man page
|
| togglefun,Snapshot-method |
Man page
|
| togglep |
Man page
|
| togglep,Snapshot-method |
Man page
|
| togglez |
Man page
|
| togglez,Snapshot-method |
Man page
|
| trellis-class |
Man page
|
| trimEnds |
Man page
|
| trimEnds,FastqQuality-method |
Man page
|
| trimEnds,ShortRead-method |
Man page
|
| trimEnds,ShortReadQ-method |
Man page
|
| trimEnds,XStringQuality-method |
Man page
|
| trimEnds,XStringSet-method |
Man page
|
| trimEnds,character-method |
Man page
|
| trimLRPatterns,ShortRead-method |
Man page
|
| trimTails |
Man page
|
| trimTails,BStringSet-method |
Man page
|
| trimTails,FastqQuality-method |
Man page
|
| trimTails,ShortReadQ-method |
Man page
|
| trimTails,XStringQuality-method |
Man page
|
| trimTails,character-method |
Man page
|
| trimTailw |
Man page
|
| trimTailw,BStringSet-method |
Man page
|
| trimTailw,FastqQuality-method |
Man page
|
| trimTailw,ShortReadQ-method |
Man page
|
| trimTailw,XStringQuality-method |
Man page
|
| trimTailw,character-method |
Man page
|
| uniqueFilter |
Man page
Source code
|
| vclass |
Man page
|
| view |
Man page
|
| view,Snapshot-method |
Man page
|
| viewer |
Man page
Source code
|
| vrange |
Man page
|
| vrange,Snapshot-method |
Man page
|
| width,FastqQuality-method |
Man page
|
| width,MatrixQuality-method |
Man page
|
| width,NumericQuality-method |
Man page
|
| width,QualityScore-method |
Man page
|
| width,ShortRead-method |
Man page
|
| writeFasta |
Man page
|
| writeFasta,DNAStringSet-method |
Man page
|
| writeFasta,ShortRead-method |
Man page
|
| writeFastq |
Man page
|
| writeFastq,ShortReadQ,FastqFile-method |
Man page
|
| writeFastq,ShortReadQ,character-method |
Man page
|
| yield |
Man page
|
| yield,FastqFileReader-method |
Man page
|
| yield,FastqSampler-method |
Man page
|
| yield,FastqStreamer-method |
Man page
|
| zi |
Man page
|
| zi,SpTrellis-method |
Man page
|
| zo |
Man page
|
| zo,SpTrellis-method |
Man page
|
| zoom |
Man page
|
| zoom,Snapshot-method |
Man page
|
