API for Bioconductor/ShortRead
FASTQ input and manipulation

Global functions
!,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,ShortRead,DNAStringSet-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
Bioconductor/ShortRead documentation built on Feb. 11, 2024, 8:18 p.m.