ShortRead: FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

AuthorMartin Morgan, Michael Lawrence, Simon Anders
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.32.1

View on Bioconductor

Man pages

accessors: (Legacy) Accessors for ShortRead classes

AlignedDataFrame: (Legacy) AlignedDataFrame constructor

AlignedDataFrame-class: (Legacy) "AlignedDataFrame" representing alignment...

AlignedRead: (Legacy) Construct objects of class "AlignedRead"

AlignedRead-class: (Legacy) "AlignedRead" class for aligned short reads

alphabetByCycle: Summarize nucleotide, amino acid, or quality scores by cycle

alphabetScore: Efficiently calculate the sum of quality scores across bases

BowtieQA-class: (Legacy) Quality assessment summaries from Bowtie files

clean: Remove sequences with ambiguous nucleotides from short read...

countLines: Count lines in all (text) files in a directory whose file...

deprecated: Deprecated and defunct functions

dotQA-class: Virtual class for representing quality assessment results

dustyScore: Summarize low-complexity sequences

ExperimentPath-class: (Legacy) "ExperimentPath" class representing a file hierarchy...

FastqQA-class: Quality assessment of fastq files and ShortReadQ objects

filterFastq: Filter fastq from one file to another

Intensity-class: (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure"...

MAQMapQA-class: (Legacy) Quality assessment summaries from MAQ map files

polyn: Utilities for common, simple operations

qa: Perform quality assessment on short reads

qa2: (Updated) quality assessment reports on short reads

QA-class: (Updated) classes for representing quality assessment results

QualityScore: Construct objects indicating read or alignment quality

QualityScore-class: Quality scores for short reads and their alignments

readAligned: (Legacy) Read aligned reads and their quality scores into R...

readBaseQuality: (Legacy) Read short reads and their quality scores into R...

readBfaToc: (Legacy) Get a list of the sequences in a Maq .bfa file

readFasta: Read and write FASTA files to or from ShortRead objects

readFastq: Read and write FASTQ-formatted files

readIntensities: (Legacy) Read Illumina image intensity files

readPrb: (Legacy) Read Solexa prb files as fastq-style quality scores

readQseq: (Legacy) Read Solexa qseq files as fastq-style quality scores

readXStringColumns: Read one or more columns into XStringSet (e.g., DNAStringSet)...

renew: Renew (update) a ShortRead object with new values

report: Summarize quality assessment results into a report

RochePath-class: (Legacy) "RochePath" class representing a Roche (454)...

RocheSet-class: (Legacy) Roche (454) experiment-wide data container

RtaIntensity: (Legacy) Construct objects of class "RtaIntensity"

RtaIntensity-class: (Legacy) Class "RtaIntensity"

Sampler-class: Sampling and streaming records from fastq files

ShortRead-class: "ShortRead" class for short reads

ShortRead-deprecated: Deprecated functions from the ShortRead package

ShortRead-package: FASTQ input and manipulation.

ShortReadQ-class: "ShortReadQ" class for short reads and their quality scores

Snapshot-class: Class '"Snapshot"'

SnapshotFunction-class: Class "SnapshotFunction"

SolexaExportQA-class: (Legacy) Quality assessment summaries from Solexa export and...

SolexaIntensity: (Legacy) Construct objects of class "SolexaIntensity" and...

SolexaIntensity-class: Classes "SolexaIntensity" and "SolexaIntensityInfo"

SolexaPath-class: (Legacy) "SolexaPath" class representing a standard output...

SolexaSet-class: (Legacy) "SolexaSet" coordinating Solexa output locations...

SpTrellis-class: Class "SpTrellis"

spViewPerFeature: Tools to visualize genomic data

srdistance: Edit distances between reads and a small number of short...

srduplicated: Order, sort, and find duplicates in XStringSet objects

srFilter: Functions for user-created and built-in ShortRead filters

SRFilter-class: "SRFilter" for representing functions operating on ShortRead...

SRFilterResult-class: "SRFilterResult" for SRFilter output and statistics

SRSet-class: (Legacy) A base class for Roche experiment-wide data

SRUtil-class: ".SRUtil" and related classes

tables: Summarize XStringSet read frequencies

trimTails: Trim ends of reads based on nucleotides or qualities

Functions

accessors Man page
alignData Man page
alignDataFilter Man page
AlignedDataFrame Man page
AlignedDataFrame-class Man page
AlignedRead 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-class 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
alignQuality Man page
alignQualityFilter Man page
alphabetByCycle Man page
alphabetByCycle,BStringSet-method Man page
alphabetByCycle,FastqQuality-method Man page
alphabetByCycle,ShortRead-method Man page
alphabetByCycle,ShortReadQ-method Man page
alphabet,FastqQuality-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,AlignedDataFrame,AlignedDataFrame-method Man page
append,AlignedRead,AlignedRead-method Man page
append,MatrixQuality,MatrixQuality-method Man page
append,QualityScore,QualityScore-method Man page
append,.ShortReadBase,.ShortReadBase-method Man page
append,ShortReadQ,ShortReadQ-method Man page
append,ShortRead,ShortRead-method Man page
ArrayIntensity Man page
[[,ArrayIntensity,ANY,ANY-method Man page
ArrayIntensity-class Man page
baseCallPath Man page
basePath Man page
BowtieQA-class Man page
chromosome Man page
chromosome,AlignedRead-method Man page
chromosomeFilter Man page
clean Man page
clean,DNAStringSet-method Man page
clean,ShortRead-method Man page
close.ShortReadFile Man page
coerce,AlignedRead,GAlignments-method Man page
coerce,AlignedRead,GappedReads-method Man page
coerce,AlignedRead,GRanges-method Man page
coerce,AlignedRead,RangedData-method Man page
coerce,AlignedRead,RangesList-method Man page
coerce,FastqQuality,matrix-method Man page
coerce,FastqQuality,numeric-method Man page
coerce,FastqQuality,PhredQuality-method Man page
coerce,PairwiseAlignments,AlignedRead-method Man page
coerce,SFastqQuality,matrix-method Man page
coerce,SFastqQuality,SolexaQuality-method Man page
coerce,ShortReadQ,QualityScaledDNAStringSet-method Man page
coerce,SRFilter,FilterRules-method Man page
compose Man page
countLines Man page
coverage,AlignedRead-method Man page
c,SRFilter-method Man page
dataPath Man page
defunct Man page
deprecated Man page
detail,AlignedRead-method Man page
detail,ExperimentPath-method Man page
detail,QualityScore-method Man page
detail,RochePath-method Man page
detail,.ShortReadBase-method Man page
detail,ShortRead-method Man page
detail,ShortReadQ-method Man page
detail,SolexaPath-method Man page
detail,SolexaSet-method Man page
detail,SRList-method Man page
detail,SRSet-method Man page
detail,SRVector-method Man page
dim,Intensity-method Man page
dim,MatrixQuality-method Man page
dustyFilter Man page
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
ExperimentPath Man page
ExperimentPath-class Man page
experimentPath,SRSet-method Man page
fac Man page
fac,Snapshot-method Man page
FastqFile Man page
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-class Man page
FastqQuality,missing-method Man page
FastqSampler Man page
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
files Man page
files,Snapshot-method Man page
filterFastq Man page
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
idFilter Man page
id,ShortRead-method Man page
ignore.strand Man page
ignore.strand,Snapshot-method Man page
imageAnalysisPath Man page
\%in\%,AlignedRead,RangesList-method Man page
IntegerQuality Man page
IntegerQuality-class Man page
intensity Man page
Intensity-class Man page
IntensityInfo-class Man page
[,IntensityMeasure,ANY,ANY,ANY-method Man page
[,IntensityMeasure,ANY,ANY-method Man page
[,IntensityMeasure,ANY,missing,ANY-method Man page
IntensityMeasure-class Man page
[,IntensityMeasure,missing,ANY,ANY-method Man page
[,IntensityMeasure,missing,missing,ANY-method 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,SpTrellis-method Man page
length,MatrixQuality-method Man page
length,QualityScore-method Man page
length,ShortRead-method Man page
length,SRList-method Man page
limits Man page
Logic,SRFilterResult,SRFilterResult-method Man page
MAQMapQA Man page
MAQMapQA-class Man page
MatrixQuality Man page
[,MatrixQuality,ANY,missing,ANY-method Man page
[,MatrixQuality,ANY,missing-method Man page
[[,MatrixQuality,ANY,missing-method Man page
MatrixQuality-class Man page
measurementError Man page
name Man page
name,SRFilter-method Man page
name,SRFilterResult-method Man page
names<-,SRList,character-method Man page
names,SRList-method Man page
narrow,FastqQuality-method Man page
narrow,MatrixQuality-method Man page
narrow,ShortRead-method Man page
narrow,ShortReadQ-method Man page
nFilter Man page
NumericQuality Man page
NumericQuality-class Man page
occurrenceFilter Man page
open.ShortReadFile Man page
pan Man page
pan,Snapshot-method Man page
phenoData,SRSet-method Man page
polyn Man page
polynFilter Man page
position Man page
position,AlignedRead-method Man page
positionFilter Man page
qa Man page
QA Man page
qa2 Man page
.QA2-class 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
QAAdapterContamination Man page
QAAdapterContamination-class Man page
qa,character-method Man page
.QA-class Man page
QA-class Man page
QA-class Man page
QACollate Man page
QACollate-class Man page
QACollate,missing-method Man page
QACollate,QAFastqSource-method Man page
QAData Man page
QAData-class Man page
QAFastqSource Man page
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
qa,list-method 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
QAReadQuality-class Man page
QASequenceUse Man page
QASequenceUse-class Man page
qa,ShortReadQ-method Man page
qa,SolexaPath-method Man page
QASource-class Man page
QASummary-class Man page
[,QualityScore,ANY,missing,ANY-method Man page
[,QualityScore,ANY,missing-method Man page
[[,QualityScore,ANY,missing-method Man page
QualityScore-class 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,character-method Man page
readAligned,SolexaPath-method Man page
readAligned,SolexaSet-method Man page
readBaseQuality Man page
readBaseQuality,character-method Man page
readBaseQuality,RochePath-method Man page
readBaseQuality,SolexaPath-method Man page
readBfaToc Man page
readCount Man page
readData Man page
reader Man page
readFasta Man page
readFasta,character-method Man page
readFastaQual Man page
readFastaQual,character-method Man page
readFastaQual,RochePath-method Man page
readFasta,RochePath-method Man page
readFasta,SolexaPath-method Man page
readFastq Man page
readFastq,character-method Man page
readFastq,FastqFile-method Man page
readFastq,SolexaPath-method Man page
readIndex Man page
readIntensities Man page
readIntensities,character-method Man page
readIntensities,SolexaPath-method Man page
readIntensityInfo Man page
readPath Man page
readPrb Man page
readPrb,character-method Man page
readPrb,SolexaPath-method Man page
readQseq Man page
readQseq,character-method Man page
readQseq,SolexaPath-method Man page
readQual Man page
readQual,character-method Man page
readQual,RochePath-method Man page
readXStringColumns Man page
renew Man page
renewable Man page
renewable,character-method Man page
renewable,missing-method Man page
renewable,.ShortReadBase-method Man page
renew,.ShortReadBase-method Man page
report Man page
report,ANY-method Man page
report,BowtieQA-method Man page
report,FastqQA-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
report,MAQMapQA-method Man page
report,QAAdapterContamination-method Man page
report,QAFiltered-method Man page
report,QAFlagged-method Man page
report,QAFrequentSequence-method Man page
report,QA-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
restore Man page
restore,SpTrellis-method Man page
reverseComplement,ShortReadQ-method Man page
reverse,FastqQuality-method Man page
reverse,ShortReadQ-method Man page
right,SpTrellis-method Man page
.Roche-class Man page
RochePath Man page
RochePath-class Man page
RocheSet Man page
RocheSet,character-method Man page
RocheSet-class Man page
RocheSet,RochePath-method Man page
RtaIntensity Man page
RtaIntensity-class Man page
runNames Man page
runNames,RochePath-method Man page
runNames,RochePath-method Man page
sapply,SRList-method Man page
scanPath Man page
SFastqQuality Man page
SFastqQuality,BStringSet-method Man page
SFastqQuality,character-method Man page
SFastqQuality-class Man page
SFastqQuality,missing-method Man page
ShortRead 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
.ShortReadBase-class Man page
ShortReadBase-package Man page
ShortRead-class Man page
ShortRead,DNAStringSet,BStringSet-method Man page
ShortRead,DNAStringSet,missing-method Man page
ShortReadFile-class 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
ShortRead,missing,missing-method Man page
ShortReadQ 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,ANY,missing,ShortReadQ-method Man page
ShortReadQ-class 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,ANY,ANY-method Man page
[,ShortReadQ,missing,ANY-method Man page
[,ShortReadQ,missing,missing,ANY-method Man page
[,ShortReadQ,missing,missing-method Man page
ShortReadQ,missing,missing,missing-method Man page
ShortReadQQA-class Man page
show,AlignedRead-method Man page
show,ExperimentPath-method Man page
show,FastqQuality-method Man page
show,IntensityMeasure-method Man page
show,Intensity-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,.QA-method Man page
show,QAReadQuality-method Man page
show,QASummary-method Man page
show,RochePath-method Man page
show,.ShortReadBase-method Man page
show,ShortRead-method Man page
show,SnapshotFunction-method Man page
show,Snapshot-method Man page
show,SolexaExportQA-method Man page
show,SolexaPath-method Man page
show,SolexaSet-method Man page
show,SpTrellis-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
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
SnapshotFunction-class Man page
SnapshotFunctionList Man page
SnapshotFunctionList,ANY-method Man page
SnapshotFunctionList-class Man page
SnapshotFunctionList,SnapshotFunction-method Man page
.Solexa-class Man page
SolexaExportQA Man page
SolexaExportQA-class Man page
SolexaIntensity Man page
[,SolexaIntensity,ANY,ANY,ANY-method Man page
[,SolexaIntensity,ANY,ANY-method Man page
[,SolexaIntensity,ANY,missing,ANY-method Man page
SolexaIntensity-class Man page
SolexaIntensityInfo Man page
SolexaIntensityInfo-class Man page
[,SolexaIntensity,missing,ANY,ANY-method Man page
[,SolexaIntensity,missing,missing,ANY-method Man page
solexaPath Man page
SolexaPath Man page
SolexaPath-class Man page
SolexaRealignQA-class Man page
SolexaSet Man page
SolexaSet,character-method Man page
SolexaSet-class Man page
SolexaSet,SolexaPath-method Man page
sourcePath Man page
SpTrellis Man page
SpTrellis-class Man page
spViewPerFeature Man page
srapply Man page
srdistance Man page
srdistance,DNAStringSet,character-method Man page
srdistance,DNAStringSet,DNAString-method Man page
srdistance,DNAStringSet,DNAStringSet-method Man page
srdistanceFilter Man page
srdistance,ShortRead,ANY-method Man page
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
SRError Man page
SRError-class Man page
srFilter Man page
SRFilter-class Man page
srFilter,function-method Man page
srFilter,missing-method Man page
SRFilterResult Man page
SRFilterResult-class Man page
!,SRFilterResult-method Man page
srFilter,SRFilter-method Man page
srlist Man page
SRList Man page
[,SRList,ANY,missing,ANY-method Man page
[,SRList,ANY,missing-method Man page
[[,SRList,ANY,missing-method Man page
SRList-class 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
SRSet-class Man page
srsort Man page
srsort,FastqQuality-method Man page
srsort,ShortRead-method Man page
srsort,XStringSet-method Man page
.SRUtil-class Man page
SRVector Man page
SRVector-class Man page
SRWarn Man page
SRWarn-class Man page
stats Man page
stats,SRFilterResult-method Man page
strand,AlignedRead-method Man page
strandFilter Man page
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,character-method 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
trimLRPatterns,ShortRead-method Man page
trimTails Man page
trimTails,BStringSet-method Man page
trimTails,character-method Man page
trimTails,FastqQuality-method Man page
trimTails,ShortReadQ-method Man page
trimTails,XStringQuality-method Man page
trimTailw Man page
trimTailw,BStringSet-method Man page
trimTailw,character-method Man page
trimTailw,FastqQuality-method Man page
trimTailw,ShortReadQ-method Man page
trimTailw,XStringQuality-method Man page
uniqueFilter Man page
vclass Man page
view Man page
viewer Man page
view,Snapshot-method Man page
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,character-method Man page
writeFastq,ShortReadQ,FastqFile-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
zoom Man page
zoom,Snapshot-method Man page
zo,SpTrellis-method Man page

Files

ShortRead/.Rinstignore
ShortRead/DESCRIPTION
ShortRead/NAMESPACE
ShortRead/NEWS
ShortRead/R
ShortRead/R/AllClasses-Base.R ShortRead/R/AllClasses-QA.R ShortRead/R/AllGenerics-Base.R ShortRead/R/AllGenerics-QA.R ShortRead/R/AllUtilities.R ShortRead/R/Snapshot.R ShortRead/R/SnapshotFunction-helpers.R ShortRead/R/SnapshotFunction.R ShortRead/R/SpTrellis.R ShortRead/R/filterFastq.R ShortRead/R/methods-.QA.R ShortRead/R/methods-.ShortReadBase.R ShortRead/R/methods-AlignedDataFrame.R ShortRead/R/methods-AlignedRead.R ShortRead/R/methods-BowtieQA.R ShortRead/R/methods-ExperimentPath.R ShortRead/R/methods-FastqFile.R ShortRead/R/methods-FastqFileReader.R ShortRead/R/methods-FastqQA.R ShortRead/R/methods-FastqSampler.R ShortRead/R/methods-FastqStreamer.R ShortRead/R/methods-Intensity.R ShortRead/R/methods-MAQMapQA.R ShortRead/R/methods-Misc.R ShortRead/R/methods-QA.R ShortRead/R/methods-QualityScore.R ShortRead/R/methods-RochePath.R ShortRead/R/methods-RocheSet.R ShortRead/R/methods-RtaIntensity.R ShortRead/R/methods-SRError.R ShortRead/R/methods-SRFilter.R ShortRead/R/methods-SRFilterResult.R ShortRead/R/methods-SRList.R ShortRead/R/methods-SRSet.R ShortRead/R/methods-SRVector.R ShortRead/R/methods-ShortRead.R ShortRead/R/methods-ShortReadFile.R ShortRead/R/methods-ShortReadQ.R ShortRead/R/methods-SolexaExportQA.R ShortRead/R/methods-SolexaIntensity.R ShortRead/R/methods-SolexaPath.R ShortRead/R/methods-SolexaRealignQA.R ShortRead/R/methods-SolexaSet.R ShortRead/R/qa.R ShortRead/R/qa_utilities.R ShortRead/R/readAligned.R ShortRead/R/readBaseQuality.R ShortRead/R/readBfaToc.R ShortRead/R/readIntensities.R ShortRead/R/readPrb.R ShortRead/R/readQseq.R ShortRead/R/readXStringColumns.R ShortRead/R/renew.R ShortRead/R/report.R ShortRead/R/spViewPerFeature.R ShortRead/R/trimEnds.R
ShortRead/build
ShortRead/build/vignette.rds
ShortRead/cleanup
ShortRead/configure
ShortRead/configure.ac
ShortRead/inst
ShortRead/inst/CITATION
ShortRead/inst/doc
ShortRead/inst/doc/Overview.R
ShortRead/inst/doc/Overview.Rnw
ShortRead/inst/doc/Overview.pdf
ShortRead/inst/extdata
ShortRead/inst/extdata/Data
ShortRead/inst/extdata/Data/C1-36Firecrest
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_prb.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_0001_seq.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/Bustard/s_1_1_0001_qseq.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/s_1_0001_int.txt
ShortRead/inst/extdata/Data/C1-36Firecrest/s_1_0001_nse.txt
ShortRead/inst/extdata/E-MTAB-1147
ShortRead/inst/extdata/E-MTAB-1147/ERR127302_1_subset.fastq.gz
ShortRead/inst/extdata/E-MTAB-1147/ERR127302_2_subset.fastq.gz
ShortRead/inst/extdata/bowtie
ShortRead/inst/extdata/bowtie/s_1_aligned_bowtie.txt
ShortRead/inst/extdata/maq
ShortRead/inst/extdata/maq/out.aln.1.txt
ShortRead/inst/extdata/maq/out.aln.2.txt
ShortRead/inst/script
ShortRead/inst/script/qa-test.R
ShortRead/inst/template
ShortRead/inst/template/0000-Header.html
ShortRead/inst/template/1000-Overview.html
ShortRead/inst/template/1100-Overview-SolexaRealign.html
ShortRead/inst/template/2000-RunSummary.html
ShortRead/inst/template/3000-ReadDistribution.html
ShortRead/inst/template/4000-CycleSpecific.html
ShortRead/inst/template/5000-PerTile.html
ShortRead/inst/template/6000-Alignment.html
ShortRead/inst/template/7000-MultipleAlignment.html
ShortRead/inst/template/8000-DepthOfCoverage.html
ShortRead/inst/template/9000-AdapterContamination.html
ShortRead/inst/template/9999-Footer.html
ShortRead/inst/template/QA.css
ShortRead/inst/template/QAAdapterContamination.html
ShortRead/inst/template/QAFiltered.html
ShortRead/inst/template/QAFlagged.html
ShortRead/inst/template/QAFooter.html
ShortRead/inst/template/QAFrequentSequence.html
ShortRead/inst/template/QAHeader.html
ShortRead/inst/template/QANucleotideByCycle.html
ShortRead/inst/template/QANucleotideUse.html
ShortRead/inst/template/QAQualityByCycle.html
ShortRead/inst/template/QAQualityUse.html
ShortRead/inst/template/QAReadQuality.html
ShortRead/inst/template/QASequenceUse.html
ShortRead/inst/template/QASources.html
ShortRead/inst/template/image
ShortRead/inst/template/image/bioclogo-small.gif
ShortRead/inst/template/qa_solexa.Rnw
ShortRead/inst/unitTests
ShortRead/inst/unitTests/cases
ShortRead/inst/unitTests/cases/PE_export.txt.gz
ShortRead/inst/unitTests/cases/s_1_0001_int_head.txt.p
ShortRead/inst/unitTests/cases/s_1_0001_nse_head.txt.p
ShortRead/inst/unitTests/cases/s_1_0001_pos_head.txt
ShortRead/inst/unitTests/cases/s_1_results_head.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_illegal_nucleotide.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_read_mismatch.txt
ShortRead/inst/unitTests/cases/s_1_sequence.8_lines_read_quality_mismatch.txt
ShortRead/inst/unitTests/cases/s_1_sequence.9_lines.txt
ShortRead/inst/unitTests/cases/s_1_sequence.txt
ShortRead/inst/unitTests/cases/s_2_0001_realign_3col_head.txt
ShortRead/inst/unitTests/cases/s_2_0001_realign_head.txt
ShortRead/inst/unitTests/cases/s_2_export_run_as_factor.txt
ShortRead/inst/unitTests/cases/s_2_export_toIUPAC.txt
ShortRead/inst/unitTests/cases/sanger.fastq
ShortRead/inst/unitTests/cases/soap.txt
ShortRead/inst/unitTests/cases/solexa.fastq
ShortRead/inst/unitTests/test_AlignedRead.R
ShortRead/inst/unitTests/test_AllClasses.R
ShortRead/inst/unitTests/test_FastqFile.R
ShortRead/inst/unitTests/test_Intensity.R
ShortRead/inst/unitTests/test_SRError.R
ShortRead/inst/unitTests/test_SRFilter.R
ShortRead/inst/unitTests/test_SRFilterResult.R
ShortRead/inst/unitTests/test_SRList.R
ShortRead/inst/unitTests/test_SRVector.R
ShortRead/inst/unitTests/test_ShortRead.R
ShortRead/inst/unitTests/test_ShortReadQ.R
ShortRead/inst/unitTests/test_SolexaIntensity.R
ShortRead/inst/unitTests/test_append.R
ShortRead/inst/unitTests/test_coverage.R
ShortRead/inst/unitTests/test_filterFastq.R
ShortRead/inst/unitTests/test_functions.R
ShortRead/inst/unitTests/test_qa.R
ShortRead/inst/unitTests/test_readPrb.R
ShortRead/inst/unitTests/test_readQseq.R
ShortRead/inst/unitTests/test_readXStringColumns.R
ShortRead/inst/unitTests/test_renew.R
ShortRead/inst/unitTests/test_trimEnds.R
ShortRead/inst/unitTests/test_trimTails.R
ShortRead/inst/unitTests/test_writeFastq.R
ShortRead/man
ShortRead/man/AlignedDataFrame-class.Rd ShortRead/man/AlignedDataFrame.Rd ShortRead/man/AlignedRead-class.Rd ShortRead/man/AlignedRead.Rd ShortRead/man/BowtieQA-class.Rd ShortRead/man/ExperimentPath-class.Rd ShortRead/man/FastqQA-class.Rd ShortRead/man/Intensity-class.Rd ShortRead/man/MAQMapQA-class.Rd ShortRead/man/QA-class.Rd ShortRead/man/QualityScore-class.Rd ShortRead/man/QualityScore.Rd ShortRead/man/RochePath-class.Rd ShortRead/man/RocheSet-class.Rd ShortRead/man/RtaIntensity-class.Rd ShortRead/man/RtaIntensity.Rd ShortRead/man/SRFilter-class.Rd ShortRead/man/SRFilterResult-class.Rd ShortRead/man/SRSet-class.Rd ShortRead/man/SRUtil-class.Rd ShortRead/man/Sampler-class.Rd ShortRead/man/ShortRead-class.Rd ShortRead/man/ShortRead-deprecated.Rd ShortRead/man/ShortRead-package.Rd ShortRead/man/ShortReadQ-class.Rd ShortRead/man/Snapshot-class.Rd ShortRead/man/SnapshotFunction-class.Rd ShortRead/man/SolexaExportQA-class.Rd ShortRead/man/SolexaIntensity-class.Rd ShortRead/man/SolexaIntensity.Rd ShortRead/man/SolexaPath-class.Rd ShortRead/man/SolexaSet-class.Rd ShortRead/man/SpTrellis-class.Rd ShortRead/man/accessors.Rd ShortRead/man/alphabetByCycle.Rd ShortRead/man/alphabetScore.Rd ShortRead/man/clean.Rd ShortRead/man/countLines.Rd ShortRead/man/deprecated.Rd ShortRead/man/dotQA-class.Rd ShortRead/man/dustyScore.Rd ShortRead/man/filterFastq.Rd ShortRead/man/polyn.Rd ShortRead/man/qa.Rd ShortRead/man/qa2.Rd ShortRead/man/readAligned.Rd ShortRead/man/readBaseQuality.Rd ShortRead/man/readBfaToc.Rd ShortRead/man/readFasta.Rd ShortRead/man/readFastq.Rd ShortRead/man/readIntensities.Rd ShortRead/man/readPrb.Rd ShortRead/man/readQseq.Rd ShortRead/man/readXStringColumns.Rd ShortRead/man/renew.Rd ShortRead/man/report.Rd ShortRead/man/spViewPerFeature.Rd ShortRead/man/srFilter.Rd ShortRead/man/srdistance.Rd ShortRead/man/srduplicated.Rd ShortRead/man/tables.Rd ShortRead/man/trimTails.Rd
ShortRead/src
ShortRead/src/Biostrings_stubs.c
ShortRead/src/IRanges_stubs.c
ShortRead/src/Makevars.in
ShortRead/src/Makevars.win
ShortRead/src/R_init_ShortRead.c
ShortRead/src/S4Vectors_stubs.c
ShortRead/src/ShortRead.h
ShortRead/src/XVector_stubs.c
ShortRead/src/alphabet.c
ShortRead/src/call.h
ShortRead/src/const.h
ShortRead/src/io.c
ShortRead/src/io_bowtie.c
ShortRead/src/io_soap.c
ShortRead/src/maqmap_m.h
ShortRead/src/readBfaToc.cc
ShortRead/src/read_maq_map.cc
ShortRead/src/sampler.c
ShortRead/src/trim.c
ShortRead/src/trim.h
ShortRead/src/util.c
ShortRead/src/xsnap.c
ShortRead/tests
ShortRead/tests/ShortRead_unit_tests.R
ShortRead/vignettes
ShortRead/vignettes/Overview.Rnw
ShortRead/vignettes/README
ShortRead/vignettes/ShortRead_and_HilbertVis.Rnw_
ShortRead/vignettes/ShortRead_and_HilbertVis.pdf
ShortRead/vignettes/hilbert.bib
ShortRead/vignettes/images
ShortRead/vignettes/images/HilbertDisplay_GUI.pdf
ShortRead/vignettes/images/HilbertDisplay_GUI.png
ShortRead/vignettes/images/HilbertPlot_H3K4me1.pdf
ShortRead/vignettes/images/HilbertPlot_H3K4me1.png
ShortRead/vignettes/images/HilbertPlot_H3K4me3.pdf
ShortRead/vignettes/images/HilbertPlot_H3K4me3.png
ShortRead/vignettes/images/Strand_and_Dir.pdf
ShortRead/vignettes/images/hilbert_3col.pdf
ShortRead/vignettes/images/hilbert_3col.png
ShortRead/vignettes/qa_E-MTAB-1147.Rda
ShortRead/vignettes/simon2.bst

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