/usr/lib/R/site-library/ShortRead/help/AnIndex is in r-bioc-shortread 1.36.0-1.
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!,SRFilterResult-method SRFilterResult-class
%in%,AlignedRead,RangesList-method AlignedRead-class
.QA-class dotQA-class
.QA2-class QA-class
.Roche-class ShortRead-package
.ShortReadBase-class ShortRead-package
.Solexa-class ShortRead-package
.SRUtil-class SRUtil-class
accessors accessors
alignData accessors
alignDataFilter srFilter
AlignedDataFrame AlignedDataFrame
AlignedDataFrame-class AlignedDataFrame-class
AlignedRead AlignedRead
AlignedRead-class AlignedRead-class
alignQuality accessors
alignQualityFilter srFilter
alphabet,FastqQuality-method QualityScore-class
alphabetByCycle alphabetByCycle
alphabetByCycle,BStringSet-method alphabetByCycle
alphabetByCycle,FastqQuality-method QualityScore-class
alphabetByCycle,ShortRead-method ShortRead-class
alphabetByCycle,ShortReadQ-method ShortReadQ-class
alphabetFrequency,FastqQuality-method QualityScore-class
alphabetScore alphabetScore
alphabetScore,FastqQuality-method QualityScore-class
alphabetScore,PhredQuality-method QualityScore-class
alphabetScore,SFastqQuality-method QualityScore-class
alphabetScore,ShortReadQ-method ShortReadQ-class
analysisPath accessors
annTrack Snapshot-class
annTrack,Snapshot-method Snapshot-class
append,.ShortReadBase,.ShortReadBase-method ShortRead-package
append,AlignedDataFrame,AlignedDataFrame-method AlignedDataFrame-class
append,AlignedRead,AlignedRead-method AlignedRead-class
append,MatrixQuality,MatrixQuality-method QualityScore-class
append,QualityScore,QualityScore-method QualityScore-class
append,ShortRead,ShortRead-method ShortRead-class
append,ShortReadQ,ShortReadQ-method ShortReadQ-class
ArrayIntensity Intensity-class
ArrayIntensity-class Intensity-class
baseCallPath accessors
basePath deprecated
BowtieQA-class BowtieQA-class
c,SRFilter-method SRFilter-class
chromosome accessors
chromosome,AlignedRead-method AlignedRead-class
chromosomeFilter srFilter
clean clean
clean,DNAStringSet-method clean
clean,ShortRead-method ShortRead-class
close.ShortReadFile Sampler-class
coerce,AlignedRead,GAlignments-method AlignedRead-class
coerce,AlignedRead,GappedReads-method AlignedRead-class
coerce,AlignedRead,GRanges-method AlignedRead-class
coerce,AlignedRead,RangedData-method AlignedRead-class
coerce,AlignedRead,RangesList-method AlignedRead-class
coerce,FastqQuality,matrix-method QualityScore-class
coerce,FastqQuality,numeric-method QualityScore-class
coerce,FastqQuality,PhredQuality-method QualityScore-class
coerce,PairwiseAlignments,AlignedRead-method AlignedRead-class
coerce,SFastqQuality,matrix-method QualityScore-class
coerce,SFastqQuality,SolexaQuality-method QualityScore-class
coerce,ShortReadQ,QualityScaledDNAStringSet-method ShortReadQ-class
coerce,SRFilter,FilterRules-method SRFilter-class
compose srFilter
countLines countLines
coverage,AlignedRead-method AlignedRead-class
dataPath accessors
defunct deprecated
deprecated deprecated
detail,.ShortReadBase-method SRUtil-class
detail,AlignedRead-method AlignedRead-class
detail,ExperimentPath-method ExperimentPath-class
detail,QualityScore-method QualityScore-class
detail,RochePath-method RochePath-class
detail,ShortRead-method ShortRead-class
detail,ShortReadQ-method ShortReadQ-class
detail,SolexaPath-method SolexaPath-class
detail,SolexaSet-method SolexaSet-class
detail,SRList-method SRUtil-class
detail,SRSet-method SRSet-class
detail,SRVector-method SRUtil-class
dim,Intensity-method Intensity-class
dim,MatrixQuality-method QualityScore-class
dustyFilter srFilter
dustyScore dustyScore
dustyScore,DNAStringSet-method dustyScore
dustyScore,ShortRead-method dustyScore
encoding,FastqQuality-method QualityScore-class
encoding,SFastqQuality-method QualityScore-class
ExperimentPath ExperimentPath-class
experimentPath accessors
experimentPath,SRSet-method SRSet-class
ExperimentPath-class ExperimentPath-class
fac Snapshot-class
fac,Snapshot-method Snapshot-class
FastqFile Sampler-class
FastqFile-class Sampler-class
FastqFileList Sampler-class
FastqFileList,ANY-method Sampler-class
FastqFileList,character-method Sampler-class
FastqFileList-class Sampler-class
FastqFileReader-class Sampler-class
FastqQA FastqQA-class
FastqQA-class FastqQA-class
FastqQuality QualityScore
FastqQuality,BStringSet-method QualityScore
FastqQuality,character-method QualityScore
FastqQuality,missing-method QualityScore
FastqQuality-class QualityScore-class
FastqSampler Sampler-class
FastqSampler-class Sampler-class
FastqSamplerList Sampler-class
FastqSamplerList,ANY-method Sampler-class
FastqSamplerList,character-method Sampler-class
FastqSamplerList-class Sampler-class
FastqStreamer Sampler-class
FastqStreamer,ANY,IRanges-method Sampler-class
FastqStreamer,ANY,missing-method Sampler-class
FastqStreamer,ANY,numeric-method Sampler-class
FastqStreamer-class Sampler-class
FastqStreamerList Sampler-class
FastqStreamerList,ANY-method Sampler-class
FastqStreamerList,character-method Sampler-class
FastqStreamerList-class Sampler-class
files Snapshot-class
files,Snapshot-method Snapshot-class
filterFastq filterFastq
flag qa2
flag,.QA2-method qa2
flag,QAFrequentSequence-method qa2
flag,QAReadQuality-method qa2
flag,QASource-method qa2
functions Snapshot-class
functions,Snapshot-method Snapshot-class
getTrellis Snapshot-class
getTrellis,Snapshot-method Snapshot-class
id accessors
id,ShortRead-method ShortRead-class
idFilter srFilter
ignore.strand Snapshot-class
ignore.strand,Snapshot-method Snapshot-class
imageAnalysisPath accessors
IntegerQuality QualityScore
IntegerQuality-class QualityScore-class
intensity Intensity-class
Intensity-class Intensity-class
IntensityInfo-class Intensity-class
IntensityMeasure-class Intensity-class
laneDescription accessors
laneNames accessors
laneNames,AnnotatedDataFrame-method SolexaSet-class
laneNames,SolexaSet-method SolexaSet-class
lapply,SRList,ANY-method SRUtil-class
lapply,SRList-method SRUtil-class
left,SpTrellis-method SpTrellis-class
length,MatrixQuality-method QualityScore-class
length,QualityScore-method QualityScore-class
length,ShortRead-method ShortRead-class
length,SRList-method SRUtil-class
limits SnapshotFunction-class
Logic,SRFilterResult,SRFilterResult-method SRFilterResult-class
MAQMapQA MAQMapQA-class
MAQMapQA-class MAQMapQA-class
MatrixQuality QualityScore
MatrixQuality-class QualityScore-class
measurementError Intensity-class
name SRFilter-class
name,SRFilter-method SRFilter-class
name,SRFilterResult-method SRFilterResult-class
names,SRList-method SRUtil-class
names<-,SRList,character-method SRUtil-class
narrow,FastqQuality-method QualityScore-class
narrow,MatrixQuality-method QualityScore-class
narrow,ShortRead-method ShortRead-class
narrow,ShortReadQ-method ShortReadQ-class
nFilter srFilter
NumericQuality QualityScore
NumericQuality-class QualityScore-class
occurrenceFilter srFilter
open.ShortReadFile Sampler-class
pan Snapshot-class
pan,Snapshot-method Snapshot-class
phenoData,SRSet-method SRSet-class
polyn polyn
polynFilter srFilter
position accessors
position,AlignedRead-method AlignedRead-class
positionFilter srFilter
QA qa2
qa qa
qa,character-method qa
qa,list-method qa
qa,ShortReadQ-method ShortReadQ-class
qa,SolexaPath-method SolexaPath-class
QA-class QA-class
qa2 qa2
qa2,FastqSampler-method qa2
qa2,QAAdapterContamination-method qa2
qa2,QACollate-method qa2
qa2,QAFastqSource-method qa2
qa2,QAFrequentSequence-method qa2
qa2,QANucleotideByCycle-method qa2
qa2,QANucleotideUse-method qa2
qa2,QAQualityByCycle-method qa2
qa2,QAQualityUse-method qa2
qa2,QAReadQuality-method qa2
qa2,QASequenceUse-method qa2
QAAdapterContamination qa2
QAAdapterContamination-class QA-class
QACollate qa2
QACollate,missing-method qa2
QACollate,QAFastqSource-method qa2
QACollate-class QA-class
QAData qa2
QAData-class QA-class
QAFastqSource qa2
QAFastqSource-class QA-class
QAFiltered qa2
QAFiltered-class QA-class
QAFlagged qa2
QAFlagged-class QA-class
QAFrequentSequence qa2
QAFrequentSequence-class QA-class
QANucleotideByCycle qa2
QANucleotideByCycle-class QA-class
QANucleotideUse qa2
QANucleotideUse-class QA-class
QAQualityByCycle qa2
QAQualityByCycle-class QA-class
QAQualityUse qa2
QAQualityUse-class QA-class
QAReadQuality qa2
QAReadQuality-class QA-class
QASequenceUse qa2
QASequenceUse-class QA-class
QASource-class QA-class
QASummary-class QA-class
QualityScore-class QualityScore-class
qualPath RochePath-class
rbind,.QA-method dotQA-class
rbind,QASummary-method qa2
read454 RochePath-class
read454,RochePath-method RochePath-class
readAligned readAligned
readAligned,BamFile-method deprecated
readAligned,character-method readAligned
readAligned,SolexaPath-method SolexaPath-class
readAligned,SolexaSet-method SolexaSet-class
readBaseQuality readBaseQuality
readBaseQuality,character-method readBaseQuality
readBaseQuality,RochePath-method RochePath-class
readBaseQuality,SolexaPath-method SolexaPath-class
readBfaToc readBfaToc
readCount SRSet-class
readData SRSet-class
reader SnapshotFunction-class
readFasta readFasta
readFasta,character-method readFasta
readFasta,RochePath-method RochePath-class
readFasta,SolexaPath-method SolexaPath-class
readFastaQual RochePath-class
readFastaQual,character-method RochePath-class
readFastaQual,RochePath-method RochePath-class
readFastq readFastq
readFastq,character-method readFastq
readFastq,FastqFile-method Sampler-class
readFastq,SolexaPath-method SolexaPath-class
readIndex SRSet-class
readIntensities readIntensities
readIntensities,character-method readIntensities
readIntensities,SolexaPath-method SolexaPath-class
readIntensityInfo Intensity-class
readPath RochePath-class
readPrb readPrb
readPrb,character-method readPrb
readPrb,SolexaPath-method SolexaPath-class
readQseq readQseq
readQseq,character-method readQseq
readQseq,SolexaPath-method SolexaPath-class
readQual RochePath-class
readQual,character-method RochePath-class
readQual,RochePath-method RochePath-class
readXStringColumns readXStringColumns
renew renew
renew,.ShortReadBase-method renew
renewable renew
renewable,.ShortReadBase-method renew
renewable,character-method renew
renewable,missing-method renew
report report
report,ANY-method report
report,BowtieQA-method BowtieQA-class
report,FastqQA-method FastqQA-class
report,MAQMapQA-method MAQMapQA-class
report,QA-method qa2
report,QAAdapterContamination-method qa2
report,QAFiltered-method qa2
report,QAFlagged-method qa2
report,QAFrequentSequence-method qa2
report,QANucleotideByCycle-method qa2
report,QANucleotideUse-method qa2
report,QAQualityByCycle-method qa2
report,QAQualityUse-method qa2
report,QAReadQuality-method qa2
report,QASequenceUse-method qa2
report,QASource-method qa2
report,SolexaExportQA-method SolexaExportQA-class
report,SolexaPath-method SolexaPath-class
report_html report
report_html,BowtieQA-method BowtieQA-class
report_html,FastqQA-method FastqQA-class
report_html,MAQMapQA-method MAQMapQA-class
report_html,ShortReadQQA-method FastqQA-class
report_html,SolexaExportQA-method SolexaExportQA-class
report_html,SolexaRealignQA-method SolexaExportQA-class
restore SpTrellis-class
restore,SpTrellis-method SpTrellis-class
reverse,FastqQuality-method QualityScore-class
reverse,ShortReadQ-method ShortReadQ-class
reverseComplement,ShortReadQ-method ShortReadQ-class
right,SpTrellis-method SpTrellis-class
RochePath RochePath-class
RochePath-class RochePath-class
RocheSet RocheSet-class
RocheSet,character-method RochePath-class
RocheSet,RochePath-method RochePath-class
RocheSet-class RocheSet-class
RtaIntensity RtaIntensity
RtaIntensity-class RtaIntensity-class
runNames RochePath-class
runNames,RochePath-method RochePath-class
sapply,SRList-method SRUtil-class
scanPath accessors
SFastqQuality QualityScore
SFastqQuality,BStringSet-method QualityScore
SFastqQuality,character-method QualityScore
SFastqQuality,missing-method QualityScore
SFastqQuality-class QualityScore-class
ShortRead ShortRead-class
ShortRead,DNAStringSet,BStringSet-method ShortRead-class
ShortRead,DNAStringSet,missing-method ShortRead-class
ShortRead,missing,missing-method ShortRead-class
ShortRead-class ShortRead-class
ShortReadFile-class Sampler-class
ShortReadQ ShortReadQ-class
ShortReadQ,DNAStringSet,BStringSet,BStringSet-method ShortReadQ-class
ShortReadQ,DNAStringSet,BStringSet,missing-method ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,BStringSet-method ShortReadQ-class
ShortReadQ,DNAStringSet,QualityScore,missing-method ShortReadQ-class
ShortReadQ,missing,missing,missing-method ShortReadQ-class
ShortReadQ-class ShortReadQ-class
ShortReadQQA-class FastqQA-class
show,.QA-method dotQA-class
show,.ShortReadBase-method ShortRead-package
show,AlignedRead-method AlignedRead-class
show,ExperimentPath-method ExperimentPath-class
show,FastqQuality-method QualityScore-class
show,Intensity-method Intensity-class
show,IntensityMeasure-method Intensity-class
show,NumericQuality-method QualityScore-class
show,QAAdapterContamination-method qa2
show,QACollate-method qa2
show,QAFastqSource-method qa2
show,QAFrequentSequence-method qa2
show,QAReadQuality-method qa2
show,QASummary-method qa2
show,RochePath-method RochePath-class
show,ShortRead-method ShortRead-class
show,Snapshot-method Snapshot-class
show,SnapshotFunction-method SnapshotFunction-class
show,SolexaExportQA-method SolexaExportQA-class
show,SolexaPath-method SolexaPath-class
show,SolexaSet-method SolexaSet-class
show,SpTrellis-method SpTrellis-class
show,SRFilter-method SRFilter-class
show,SRFilterResult-method SRFilterResult-class
show,SRList-method SRUtil-class
show,SRSet-method SRSet-class
show,SRVector-method SRUtil-class
Snapshot Snapshot-class
Snapshot,BamFileList,GRanges-method Snapshot-class
Snapshot,character,GRanges-method Snapshot-class
Snapshot,character,missing-method Snapshot-class
Snapshot-class Snapshot-class
SnapshotFunction SnapshotFunction-class
SnapshotFunction-class SnapshotFunction-class
SnapshotFunctionList SnapshotFunction-class
SnapshotFunctionList,ANY-method SnapshotFunction-class
SnapshotFunctionList,SnapshotFunction-method SnapshotFunction-class
SnapshotFunctionList-class SnapshotFunction-class
SolexaExportQA SolexaExportQA-class
SolexaExportQA-class SolexaExportQA-class
SolexaIntensity SolexaIntensity
SolexaIntensity-class SolexaIntensity-class
SolexaIntensityInfo SolexaIntensity
SolexaIntensityInfo-class SolexaIntensity-class
SolexaPath SolexaPath-class
solexaPath accessors
SolexaPath-class SolexaPath-class
SolexaRealignQA-class SolexaExportQA-class
SolexaSet SolexaSet-class
SolexaSet,character-method SolexaSet-class
SolexaSet,SolexaPath-method SolexaPath-class
SolexaSet-class SolexaSet-class
sourcePath SRSet-class
SpTrellis SpTrellis-class
SpTrellis-class SpTrellis-class
spViewPerFeature spViewPerFeature
srapply deprecated
srdistance srdistance
srdistance,DNAStringSet,character-method srdistance
srdistance,DNAStringSet,DNAString-method srdistance
srdistance,DNAStringSet,DNAStringSet-method srdistance
srdistance,ShortRead,ANY-method ShortRead-class
srdistanceFilter srFilter
srduplicated srduplicated
srduplicated,AlignedRead-method AlignedRead-class
srduplicated,FastqQuality-method QualityScore-class
srduplicated,ShortRead-method ShortRead-class
srduplicated,XStringSet-method srduplicated
sread accessors
sread,ShortRead-method accessors
SRError SRUtil-class
SRError-class SRUtil-class
srFilter srFilter
srFilter,function-method srFilter
srFilter,missing-method srFilter
srFilter,SRFilter-method SRFilter-class
SRFilter-class SRFilter-class
SRFilterResult SRFilterResult-class
SRFilterResult-class SRFilterResult-class
SRList SRUtil-class
srlist SRUtil-class
SRList-class SRUtil-class
srorder srduplicated
srorder,AlignedRead-method AlignedRead-class
srorder,FastqQuality-method QualityScore-class
srorder,ShortRead-method ShortRead-class
srorder,XStringSet-method srduplicated
srrank srduplicated
srrank,AlignedRead-method AlignedRead-class
srrank,FastqQuality-method QualityScore-class
srrank,ShortRead-method ShortRead-class
srrank,XStringSet-method srduplicated
SRSet-class SRSet-class
srsort srduplicated
srsort,FastqQuality-method QualityScore-class
srsort,ShortRead-method ShortRead-class
srsort,XStringSet-method srduplicated
SRVector SRUtil-class
SRVector-class SRUtil-class
SRWarn SRUtil-class
SRWarn-class SRUtil-class
stats SRFilterResult-class
stats,SRFilterResult-method SRFilterResult-class
strand,AlignedRead-method AlignedRead-class
strandFilter srFilter
tables tables
tables,ShortRead-method ShortRead-class
tables,XStringSet-method tables
togglefun Snapshot-class
togglefun,Snapshot-method Snapshot-class
togglep Snapshot-class
togglep,Snapshot-method Snapshot-class
togglez Snapshot-class
togglez,Snapshot-method Snapshot-class
trellis-class Snapshot-class
trimEnds trimTails
trimEnds,character-method trimTails
trimEnds,FastqQuality-method trimTails
trimEnds,ShortRead-method trimTails
trimEnds,ShortReadQ-method trimTails
trimEnds,XStringQuality-method trimTails
trimEnds,XStringSet-method trimTails
trimLRPatterns,ShortRead-method ShortRead-class
trimTails trimTails
trimTails,BStringSet-method trimTails
trimTails,character-method trimTails
trimTails,FastqQuality-method QualityScore-class
trimTails,ShortReadQ-method ShortReadQ-class
trimTails,XStringQuality-method trimTails
trimTailw trimTails
trimTailw,BStringSet-method trimTails
trimTailw,character-method trimTails
trimTailw,FastqQuality-method QualityScore-class
trimTailw,ShortReadQ-method ShortReadQ-class
trimTailw,XStringQuality-method trimTails
uniqueFilter ShortRead-deprecated
vclass accessors
view Snapshot-class
view,Snapshot-method Snapshot-class
viewer SnapshotFunction-class
vrange Snapshot-class
vrange,Snapshot-method Snapshot-class
width,FastqQuality-method QualityScore-class
width,MatrixQuality-method QualityScore-class
width,NumericQuality-method QualityScore-class
width,QualityScore-method QualityScore-class
width,ShortRead-method ShortRead-class
writeFasta readFasta
writeFasta,DNAStringSet-method readFasta
writeFasta,ShortRead-method ShortRead-class
writeFastq readFastq
writeFastq,ShortReadQ,character-method ShortReadQ-class
writeFastq,ShortReadQ,FastqFile-method ShortReadQ-class
yield Sampler-class
yield,FastqFileReader-method Sampler-class
yield,FastqSampler-method Sampler-class
yield,FastqStreamer-method Sampler-class
zi SpTrellis-class
zi,SpTrellis-method SpTrellis-class
zo SpTrellis-class
zo,SpTrellis-method SpTrellis-class
zoom Snapshot-class
zoom,Snapshot-method Snapshot-class
[,AlignedRead,ANY,ANY,ANY-method AlignedRead-class
[,AlignedRead,ANY,ANY-method AlignedRead-class
[,AlignedRead,ANY,missing,ANY-method AlignedRead-class
[,AlignedRead,ANY,missing-method AlignedRead-class
[,AlignedRead,missing,ANY,ANY-method AlignedRead-class
[,AlignedRead,missing,ANY-method AlignedRead-class
[,AlignedRead,missing,missing,ANY-method AlignedRead-class
[,AlignedRead,missing,missing-method AlignedRead-class
[,IntensityMeasure,ANY,ANY,ANY-method Intensity-class
[,IntensityMeasure,ANY,ANY-method Intensity-class
[,IntensityMeasure,ANY,missing,ANY-method Intensity-class
[,IntensityMeasure,missing,ANY,ANY-method Intensity-class
[,IntensityMeasure,missing,missing,ANY-method Intensity-class
[,MatrixQuality,ANY,missing,ANY-method QualityScore-class
[,MatrixQuality,ANY,missing-method QualityScore-class
[,QualityScore,ANY,missing,ANY-method QualityScore-class
[,QualityScore,ANY,missing-method QualityScore-class
[,ShortRead,ANY,ANY,ANY-method ShortRead-class
[,ShortRead,ANY,ANY-method ShortRead-class
[,ShortRead,ANY,missing,ANY-method ShortRead-class
[,ShortRead,ANY,missing-method ShortRead-class
[,ShortRead,missing,ANY,ANY-method ShortRead-class
[,ShortRead,missing,ANY-method ShortRead-class
[,ShortRead,missing,missing,ANY-method ShortRead-class
[,ShortRead,missing,missing-method ShortRead-class
[,ShortReadQ,ANY,ANY,ANY-method ShortReadQ-class
[,ShortReadQ,ANY,ANY-method ShortReadQ-class
[,ShortReadQ,ANY,missing,ANY-method ShortReadQ-class
[,ShortReadQ,ANY,missing-method ShortReadQ-class
[,ShortReadQ,missing,ANY,ANY-method ShortReadQ-class
[,ShortReadQ,missing,ANY-method ShortReadQ-class
[,ShortReadQ,missing,missing,ANY-method ShortReadQ-class
[,ShortReadQ,missing,missing-method ShortReadQ-class
[,SolexaIntensity,ANY,ANY,ANY-method SolexaIntensity-class
[,SolexaIntensity,ANY,ANY-method SolexaIntensity-class
[,SolexaIntensity,ANY,missing,ANY-method SolexaIntensity-class
[,SolexaIntensity,missing,ANY,ANY-method SolexaIntensity-class
[,SolexaIntensity,missing,missing,ANY-method SolexaIntensity-class
[,SRList,ANY,missing,ANY-method SRUtil-class
[,SRList,ANY,missing-method SRUtil-class
[<-,ShortReadQ,ANY,missing,ShortReadQ-method ShortReadQ-class
[[,ArrayIntensity,ANY,ANY-method Intensity-class
[[,MatrixQuality,ANY,missing-method QualityScore-class
[[,QualityScore,ANY,missing-method QualityScore-class
[[,SRList,ANY,missing-method SRUtil-class
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