A B C D E F G I L M N O P Q R S T U V W Y Z misc
ShortReadBase-package | Base classes and methods for high-throughput short-read sequencing data. |
accessors | Accessors for ShortRead classes |
alignData | Accessors for ShortRead classes |
alignDataFilter | Functions for user-created and built-in ShortRead filters |
AlignedDataFrame | AlignedDataFrame constructor |
AlignedDataFrame-class | "AlignedDataFrame" representing alignment annotations as a data frame |
AlignedRead | Construct objects of class "AlignedRead" |
AlignedRead-class | "AlignedRead" class for aligned short reads |
alignQuality | Accessors for ShortRead classes |
alignQualityFilter | Functions for user-created and built-in ShortRead filters |
alphabet-method | Quality scores for short reads and their alignments |
alphabetByCycle | Summarize short read nucleotide or quality scores by cycle |
alphabetByCycle-method | Quality scores for short reads and their alignments |
alphabetByCycle-method | "ShortRead" class for short reads |
alphabetByCycle-method | "ShortReadQ" class for short reads and their quality scores |
alphabetByCycle-method | Summarize short read nucleotide or quality scores by cycle |
alphabetFrequency-method | Quality scores for short reads and their alignments |
alphabetScore | Efficiently calculate the sum of quality scores across bases |
alphabetScore-method | Quality scores for short reads and their alignments |
alphabetScore-method | "ShortReadQ" class for short reads and their quality scores |
analysisPath | Accessors for ShortRead classes |
annTrack | Class '"Snapshot"' |
annTrack-method | Class '"Snapshot"' |
append-method | "AlignedDataFrame" representing alignment annotations as a data frame |
append-method | "AlignedRead" class for aligned short reads |
append-method | Quality scores for short reads and their alignments |
append-method | "ShortRead" class for short reads |
append-method | Base classes and methods for high-throughput short-read sequencing data. |
append-method | "ShortReadQ" class for short reads and their quality scores |
ArrayIntensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
ArrayIntensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
BAMQA-class | Quality assessment from BAM files |
baseCallPath | Accessors for ShortRead classes |
basePath | Deprecated and defunct functions |
BowtieQA-class | Quality assessment summaries from Bowtie files |
c-method | GappedReads objects |
c-method | "SRFilter" for representing functions operating on ShortRead objects |
chromosome | Accessors for ShortRead classes |
chromosome-method | "AlignedRead" class for aligned short reads |
chromosomeFilter | Functions for user-created and built-in ShortRead filters |
class:GappedReads | GappedReads objects |
clean | Remove sequences with ambiguous nucleotides from short read classes |
clean-method | "ShortRead" class for short reads |
clean-method | Remove sequences with ambiguous nucleotides from short read classes |
close.ShortReadFile | Sampling and streaming records from fastq files |
coerce-method | "AlignedRead" class for aligned short reads |
coerce-method | Quality scores for short reads and their alignments |
coerce-method | "SRFilter" for representing functions operating on ShortRead objects |
coerce-method | "ShortReadQ" class for short reads and their quality scores |
compose | Functions for user-created and built-in ShortRead filters |
countLines | Count lines in all (text) files in a directory whose file name matches a pattern |
coverage-method | "AlignedRead" class for aligned short reads |
dataPath | Accessors for ShortRead classes |
defunct | Deprecated and defunct functions |
deprecated | Deprecated and defunct functions |
detail-method | "AlignedRead" class for aligned short reads |
detail-method | "ExperimentPath" class representing a file hierarchy of data files |
detail-method | Quality scores for short reads and their alignments |
detail-method | "RochePath" class representing a Roche (454) experiment location |
detail-method | A base class for Roche experiment-wide data |
detail-method | ".SRUtil" and related classes |
detail-method | "ShortRead" class for short reads |
detail-method | "ShortReadQ" class for short reads and their quality scores |
detail-method | "SolexaPath" class representing a standard output file hierarchy |
detail-method | "SolexaSet" coordinating Solexa output locations with sample annotations |
dim-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
dim-method | Quality scores for short reads and their alignments |
dustyFilter | Functions for user-created and built-in ShortRead filters |
dustyScore | Summarize low-complexity sequences |
dustyScore-method | Summarize low-complexity sequences |
ExperimentPath | "ExperimentPath" class representing a file hierarchy of data files |
experimentPath | Accessors for ShortRead classes |
ExperimentPath-class | "ExperimentPath" class representing a file hierarchy of data files |
experimentPath-method | A base class for Roche experiment-wide data |
fac | Class '"Snapshot"' |
fac-method | Class '"Snapshot"' |
FastqFile | Sampling and streaming records from fastq files |
FastqFile-class | Sampling and streaming records from fastq files |
FastqFileList | Sampling and streaming records from fastq files |
FastqFileList-class | Sampling and streaming records from fastq files |
FastqFileList-method | Sampling and streaming records from fastq files |
FastqFileReader-class | Sampling and streaming records from fastq files |
FastqQA | Quality assessment of fastq files and ShortReadQ objects |
FastqQA-class | Quality assessment of fastq files and ShortReadQ objects |
FastqQuality | Construct objects indicating read or alignment quality |
FastqQuality-class | Quality scores for short reads and their alignments |
FastqQuality-method | Construct objects indicating read or alignment quality |
FastqSampler | Sampling and streaming records from fastq files |
FastqSampler-class | Sampling and streaming records from fastq files |
FastqSamplerList | Sampling and streaming records from fastq files |
FastqSamplerList-class | Sampling and streaming records from fastq files |
FastqSamplerList-method | Sampling and streaming records from fastq files |
FastqStreamer | Sampling and streaming records from fastq files |
FastqStreamer-class | Sampling and streaming records from fastq files |
FastqStreamer-method | Sampling and streaming records from fastq files |
FastqStreamerList | Sampling and streaming records from fastq files |
FastqStreamerList-class | Sampling and streaming records from fastq files |
FastqStreamerList-method | Sampling and streaming records from fastq files |
files | Class '"Snapshot"' |
files-method | Class '"Snapshot"' |
flag | (Updated) quality assessment reports on short reads |
flag-method | (Updated) quality assessment reports on short reads |
functions | Class '"Snapshot"' |
functions-method | Class '"Snapshot"' |
GappedReads | GappedReads objects |
GappedReads-class | GappedReads objects |
getTrellis | Class '"Snapshot"' |
getTrellis-method | Class '"Snapshot"' |
id | Accessors for ShortRead classes |
id-method | "ShortRead" class for short reads |
idFilter | Functions for user-created and built-in ShortRead filters |
ignore.strand | Class '"Snapshot"' |
ignore.strand-method | Class '"Snapshot"' |
imageAnalysisPath | Accessors for ShortRead classes |
IntegerQuality | Construct objects indicating read or alignment quality |
IntegerQuality-class | Quality scores for short reads and their alignments |
intensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
Intensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
IntensityInfo-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
IntensityMeasure-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
laneDescription | Accessors for ShortRead classes |
laneNames | Accessors for ShortRead classes |
laneNames-method | "SolexaSet" coordinating Solexa output locations with sample annotations |
lapply-method | ".SRUtil" and related classes |
left-method | Class "SpTrellis" |
length-method | Quality scores for short reads and their alignments |
length-method | ".SRUtil" and related classes |
length-method | "ShortRead" class for short reads |
limits | Class "SnapshotFunction" |
Logic-method | "SRFilterResult" for SRFilter output and statistics |
MAQMapQA | Quality assessment summaries from MAQ map files |
MAQMapQA-class | Quality assessment summaries from MAQ map files |
MatrixQuality | Construct objects indicating read or alignment quality |
MatrixQuality-class | Quality scores for short reads and their alignments |
measurementError | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
name | "SRFilter" for representing functions operating on ShortRead objects |
name-method | "SRFilter" for representing functions operating on ShortRead objects |
name-method | "SRFilterResult" for SRFilter output and statistics |
names-method | ".SRUtil" and related classes |
names<--method | ".SRUtil" and related classes |
narrow-method | GappedReads objects |
narrow-method | Quality scores for short reads and their alignments |
narrow-method | "ShortRead" class for short reads |
narrow-method | "ShortReadQ" class for short reads and their quality scores |
nFilter | Functions for user-created and built-in ShortRead filters |
NumericQuality | Construct objects indicating read or alignment quality |
NumericQuality-class | Quality scores for short reads and their alignments |
occurrenceFilter | Functions for user-created and built-in ShortRead filters |
open.ShortReadFile | Sampling and streaming records from fastq files |
pan | Class '"Snapshot"' |
pan-method | Class '"Snapshot"' |
phenoData-method | A base class for Roche experiment-wide data |
pileup | Deprecated and defunct functions |
polyn | Utilities for common, simple operations |
polynFilter | Functions for user-created and built-in ShortRead filters |
position | Accessors for ShortRead classes |
position-method | "AlignedRead" class for aligned short reads |
positionFilter | Functions for user-created and built-in ShortRead filters |
QA | (Updated) quality assessment reports on short reads |
qa | Perform quality assessment on short reads |
QA-class | (Updated) classes for representing quality assessment results |
qa-method | "ShortReadQ" class for short reads and their quality scores |
qa-method | "SolexaPath" class representing a standard output file hierarchy |
qa-method | Perform quality assessment on short reads |
qa2 | (Updated) quality assessment reports on short reads |
qa2-method | (Updated) quality assessment reports on short reads |
QAAdapterContamination | (Updated) quality assessment reports on short reads |
QAAdapterContamination-class | (Updated) classes for representing quality assessment results |
QACollate | (Updated) quality assessment reports on short reads |
QACollate-class | (Updated) classes for representing quality assessment results |
QACollate-method | (Updated) quality assessment reports on short reads |
QAData | (Updated) quality assessment reports on short reads |
QAData-class | (Updated) classes for representing quality assessment results |
QAFastqSource | (Updated) quality assessment reports on short reads |
QAFastqSource-class | (Updated) classes for representing quality assessment results |
QAFiltered | (Updated) quality assessment reports on short reads |
QAFiltered-class | (Updated) classes for representing quality assessment results |
QAFlagged | (Updated) quality assessment reports on short reads |
QAFlagged-class | (Updated) classes for representing quality assessment results |
QAFrequentSequence | (Updated) quality assessment reports on short reads |
QAFrequentSequence-class | (Updated) classes for representing quality assessment results |
QANucleotideByCycle | (Updated) quality assessment reports on short reads |
QANucleotideByCycle-class | (Updated) classes for representing quality assessment results |
QANucleotideUse | (Updated) quality assessment reports on short reads |
QANucleotideUse-class | (Updated) classes for representing quality assessment results |
QAQualityByCycle | (Updated) quality assessment reports on short reads |
QAQualityByCycle-class | (Updated) classes for representing quality assessment results |
QAQualityUse | (Updated) quality assessment reports on short reads |
QAQualityUse-class | (Updated) classes for representing quality assessment results |
QAReadQuality | (Updated) quality assessment reports on short reads |
QAReadQuality-class | (Updated) classes for representing quality assessment results |
QASequenceUse | (Updated) quality assessment reports on short reads |
QASequenceUse-class | (Updated) classes for representing quality assessment results |
QASource-class | (Updated) classes for representing quality assessment results |
QASummary-class | (Updated) classes for representing quality assessment results |
qnarrow-method | GappedReads objects |
qseq | GappedReads objects |
qseq-method | GappedReads objects |
QualityScore-class | Quality scores for short reads and their alignments |
qualPath | "RochePath" class representing a Roche (454) experiment location |
qwidth-method | GappedReads objects |
rbind-method | Virtual class for representing quality assessment results |
rbind-method | (Updated) quality assessment reports on short reads |
read454 | "RochePath" class representing a Roche (454) experiment location |
read454-method | "RochePath" class representing a Roche (454) experiment location |
readAligned | Read aligned reads and their quality scores into R representations |
readAligned-method | "SolexaPath" class representing a standard output file hierarchy |
readAligned-method | "SolexaSet" coordinating Solexa output locations with sample annotations |
readAligned-method | Read aligned reads and their quality scores into R representations |
readBaseQuality | Read short reads and their quality scores into R representations |
readBaseQuality-method | "RochePath" class representing a Roche (454) experiment location |
readBaseQuality-method | "SolexaPath" class representing a standard output file hierarchy |
readBaseQuality-method | Read short reads and their quality scores into R representations |
readBfaToc | Get a list of the sequences in a Maq .bfa file |
readCount | A base class for Roche experiment-wide data |
readData | A base class for Roche experiment-wide data |
reader | Class "SnapshotFunction" |
readFasta | Read and write FASTA files to or from ShortRead objects |
readFasta-method | "RochePath" class representing a Roche (454) experiment location |
readFasta-method | "SolexaPath" class representing a standard output file hierarchy |
readFasta-method | Read and write FASTA files to or from ShortRead objects |
readFastaQual | "RochePath" class representing a Roche (454) experiment location |
readFastaQual-method | "RochePath" class representing a Roche (454) experiment location |
readFastq | Read and write FASTQ-formatted files |
readFastq-method | Sampling and streaming records from fastq files |
readFastq-method | "SolexaPath" class representing a standard output file hierarchy |
readFastq-method | Read and write FASTQ-formatted files |
readGappedReads | GappedReads objects |
readIndex | A base class for Roche experiment-wide data |
readInfo | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
readIntensities | Read Illumina image intensity files |
readIntensities-method | "SolexaPath" class representing a standard output file hierarchy |
readIntensities-method | Read Illumina image intensity files |
readPath | "RochePath" class representing a Roche (454) experiment location |
readPrb | Read Solexa prb files as fastq-style quality scores |
readPrb-method | "SolexaPath" class representing a standard output file hierarchy |
readPrb-method | Read Solexa prb files as fastq-style quality scores |
readQseq | Read Solexa qseq files as fastq-style quality scores |
readQseq-method | "SolexaPath" class representing a standard output file hierarchy |
readQseq-method | Read Solexa qseq files as fastq-style quality scores |
readQual | "RochePath" class representing a Roche (454) experiment location |
readQual-method | "RochePath" class representing a Roche (454) experiment location |
readXStringColumns | Read one or more columns into XStringSet (e.g., DNAStringSet) objects |
renew | Renew (update) a ShortRead object with new values |
renew-method | Renew (update) a ShortRead object with new values |
renewable | Renew (update) a ShortRead object with new values |
renewable-method | Renew (update) a ShortRead object with new values |
report | Summarize quality assessment results into a report |
report-method | Quality assessment from BAM files |
report-method | Quality assessment summaries from Bowtie files |
report-method | Quality assessment of fastq files and ShortReadQ objects |
report-method | Quality assessment summaries from MAQ map files |
report-method | Quality assessment summaries from Solexa export and realign files |
report-method | "SolexaPath" class representing a standard output file hierarchy |
report-method | (Updated) quality assessment reports on short reads |
report-method | Summarize quality assessment results into a report |
report_html | Summarize quality assessment results into a report |
report_html-method | Quality assessment from BAM files |
report_html-method | Quality assessment summaries from Bowtie files |
report_html-method | Quality assessment of fastq files and ShortReadQ objects |
report_html-method | Quality assessment summaries from MAQ map files |
report_html-method | Quality assessment summaries from Solexa export and realign files |
restore | Class "SpTrellis" |
restore-method | Class "SpTrellis" |
right-method | Class "SpTrellis" |
RochePath | "RochePath" class representing a Roche (454) experiment location |
RochePath-class | "RochePath" class representing a Roche (454) experiment location |
RocheSet | Roche (454) experiment-wide data container |
RocheSet-class | Roche (454) experiment-wide data container |
RocheSet-method | "RochePath" class representing a Roche (454) experiment location |
RtaIntensity | Construct objects of class "RtaIntensity" |
RtaIntensity-class | Class "RtaIntensity" |
runNames | "RochePath" class representing a Roche (454) experiment location |
runNames-method | "RochePath" class representing a Roche (454) experiment location |
sapply-method | ".SRUtil" and related classes |
scanPath | Accessors for ShortRead classes |
SFastqQuality | Construct objects indicating read or alignment quality |
SFastqQuality-class | Quality scores for short reads and their alignments |
SFastqQuality-method | Construct objects indicating read or alignment quality |
ShortRead | "ShortRead" class for short reads |
ShortRead-class | "ShortRead" class for short reads |
ShortRead-method | "ShortRead" class for short reads |
ShortReadFile-class | Sampling and streaming records from fastq files |
ShortReadQ | "ShortReadQ" class for short reads and their quality scores |
ShortReadQ-class | "ShortReadQ" class for short reads and their quality scores |
ShortReadQ-method | "ShortReadQ" class for short reads and their quality scores |
ShortReadQQA-class | Quality assessment of fastq files and ShortReadQ objects |
show-method | "AlignedRead" class for aligned short reads |
show-method | "ExperimentPath" class representing a file hierarchy of data files |
show-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
show-method | Quality scores for short reads and their alignments |
show-method | "RochePath" class representing a Roche (454) experiment location |
show-method | "SRFilter" for representing functions operating on ShortRead objects |
show-method | "SRFilterResult" for SRFilter output and statistics |
show-method | A base class for Roche experiment-wide data |
show-method | ".SRUtil" and related classes |
show-method | "ShortRead" class for short reads |
show-method | Base classes and methods for high-throughput short-read sequencing data. |
show-method | Class '"Snapshot"' |
show-method | Class "SnapshotFunction" |
show-method | Quality assessment summaries from Solexa export and realign files |
show-method | "SolexaPath" class representing a standard output file hierarchy |
show-method | "SolexaSet" coordinating Solexa output locations with sample annotations |
show-method | Class "SpTrellis" |
show-method | Virtual class for representing quality assessment results |
show-method | (Updated) quality assessment reports on short reads |
Snapshot | Class '"Snapshot"' |
Snapshot-class | Class '"Snapshot"' |
Snapshot-method | Class '"Snapshot"' |
SnapshotFunction | Class "SnapshotFunction" |
SnapshotFunction-class | Class "SnapshotFunction" |
SnapshotFunctionList | Class "SnapshotFunction" |
SnapshotFunctionList-class | Class "SnapshotFunction" |
SnapshotFunctionList-method | Class "SnapshotFunction" |
SolexaExportQA | Quality assessment summaries from Solexa export and realign files |
SolexaExportQA-class | Quality assessment summaries from Solexa export and realign files |
SolexaIntensity | Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo" |
SolexaIntensity-class | Classes "SolexaIntensity" and "SolexaIntensityInfo" |
SolexaIntensityInfo | Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo" |
SolexaIntensityInfo-class | Classes "SolexaIntensity" and "SolexaIntensityInfo" |
SolexaPath | "SolexaPath" class representing a standard output file hierarchy |
solexaPath | Accessors for ShortRead classes |
SolexaPath-class | "SolexaPath" class representing a standard output file hierarchy |
SolexaRealignQA-class | Quality assessment summaries from Solexa export and realign files |
SolexaSet | "SolexaSet" coordinating Solexa output locations with sample annotations |
SolexaSet-class | "SolexaSet" coordinating Solexa output locations with sample annotations |
SolexaSet-method | "SolexaPath" class representing a standard output file hierarchy |
SolexaSet-method | "SolexaSet" coordinating Solexa output locations with sample annotations |
sourcePath | A base class for Roche experiment-wide data |
SpTrellis | Class "SpTrellis" |
SpTrellis-class | Class "SpTrellis" |
spViewPerFeature | Tools to visualize genomic data |
srapply | Apply-like function for distribution across MPI-based clusters. |
srdistance | Edit distances between reads and a small number of short references |
srdistance-method | "ShortRead" class for short reads |
srdistance-method | Edit distances between reads and a small number of short references |
srdistanceFilter | Functions for user-created and built-in ShortRead filters |
srduplicated | Order, sort, and find duplicates in XStringSet objects |
srduplicated-method | "AlignedRead" class for aligned short reads |
srduplicated-method | Quality scores for short reads and their alignments |
srduplicated-method | "ShortRead" class for short reads |
srduplicated-method | Order, sort, and find duplicates in XStringSet objects |
sread | Accessors for ShortRead classes |
SRError | ".SRUtil" and related classes |
SRError-class | ".SRUtil" and related classes |
srFilter | Functions for user-created and built-in ShortRead filters |
SRFilter-class | "SRFilter" for representing functions operating on ShortRead objects |
srFilter-method | "SRFilter" for representing functions operating on ShortRead objects |
srFilter-method | Functions for user-created and built-in ShortRead filters |
SRFilterResult | "SRFilterResult" for SRFilter output and statistics |
SRFilterResult-class | "SRFilterResult" for SRFilter output and statistics |
SRList | ".SRUtil" and related classes |
SRList-class | ".SRUtil" and related classes |
srorder | Order, sort, and find duplicates in XStringSet objects |
srorder-method | "AlignedRead" class for aligned short reads |
srorder-method | Quality scores for short reads and their alignments |
srorder-method | "ShortRead" class for short reads |
srorder-method | Order, sort, and find duplicates in XStringSet objects |
srrank | Order, sort, and find duplicates in XStringSet objects |
srrank-method | "AlignedRead" class for aligned short reads |
srrank-method | Quality scores for short reads and their alignments |
srrank-method | "ShortRead" class for short reads |
srrank-method | Order, sort, and find duplicates in XStringSet objects |
SRSet-class | A base class for Roche experiment-wide data |
srsort | Order, sort, and find duplicates in XStringSet objects |
srsort-method | Quality scores for short reads and their alignments |
srsort-method | "ShortRead" class for short reads |
srsort-method | Order, sort, and find duplicates in XStringSet objects |
SRVector | ".SRUtil" and related classes |
SRVector-class | ".SRUtil" and related classes |
SRWarn | ".SRUtil" and related classes |
SRWarn-class | ".SRUtil" and related classes |
stats | "SRFilterResult" for SRFilter output and statistics |
stats-method | "SRFilterResult" for SRFilter output and statistics |
strand-method | "AlignedRead" class for aligned short reads |
strandFilter | Functions for user-created and built-in ShortRead filters |
tables | Summarize XStringSet read frequencies |
tables-method | "ShortRead" class for short reads |
tables-method | Summarize XStringSet read frequencies |
togglefun | Class '"Snapshot"' |
togglefun-method | Class '"Snapshot"' |
togglep | Class '"Snapshot"' |
togglep-method | Class '"Snapshot"' |
togglez | Class '"Snapshot"' |
togglez-method | Class '"Snapshot"' |
trellis-class | Class '"Snapshot"' |
trimEnds | Trim ends of reads based on nucleotides or qualities |
trimEnds-method | Trim ends of reads based on nucleotides or qualities |
trimLRPatterns-method | "ShortRead" class for short reads |
trimTails | Trim ends of reads based on nucleotides or qualities |
trimTails-method | Quality scores for short reads and their alignments |
trimTails-method | "ShortReadQ" class for short reads and their quality scores |
trimTails-method | Trim ends of reads based on nucleotides or qualities |
trimTailw | Trim ends of reads based on nucleotides or qualities |
trimTailw-method | Quality scores for short reads and their alignments |
trimTailw-method | "ShortReadQ" class for short reads and their quality scores |
trimTailw-method | Trim ends of reads based on nucleotides or qualities |
uniqueFilter | Deprecated functions from the ShortRead package |
vclass | Accessors for ShortRead classes |
view | Class '"Snapshot"' |
view-method | Class '"Snapshot"' |
viewer | Class "SnapshotFunction" |
vrange | Class '"Snapshot"' |
vrange-method | Class '"Snapshot"' |
width-method | Quality scores for short reads and their alignments |
width-method | "ShortRead" class for short reads |
writeFasta | Read and write FASTA files to or from ShortRead objects |
writeFasta-method | "ShortRead" class for short reads |
writeFasta-method | Read and write FASTA files to or from ShortRead objects |
writeFastq | Read and write FASTQ-formatted files |
writeFastq-method | "ShortReadQ" class for short reads and their quality scores |
yield | Sampling and streaming records from fastq files |
yield-method | Sampling and streaming records from fastq files |
zi | Class "SpTrellis" |
zi-method | Class "SpTrellis" |
zo | Class "SpTrellis" |
zo-method | Class "SpTrellis" |
zoom | Class '"Snapshot"' |
zoom-method | Class '"Snapshot"' |
!-method | "SRFilterResult" for SRFilter output and statistics |
%in%-method | "AlignedRead" class for aligned short reads |
.QA-class | Virtual class for representing quality assessment results |
.QA2-class | (Updated) classes for representing quality assessment results |
.Roche-class | Base classes and methods for high-throughput short-read sequencing data. |
.ShortReadBase-class | Base classes and methods for high-throughput short-read sequencing data. |
.Solexa-class | Base classes and methods for high-throughput short-read sequencing data. |
.SRUtil-class | ".SRUtil" and related classes |
[-method | "AlignedRead" class for aligned short reads |
[-method | GappedReads objects |
[-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
[-method | Quality scores for short reads and their alignments |
[-method | ".SRUtil" and related classes |
[-method | "ShortRead" class for short reads |
[-method | "ShortReadQ" class for short reads and their quality scores |
[-method | Classes "SolexaIntensity" and "SolexaIntensityInfo" |
[[-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
[[-method | Quality scores for short reads and their alignments |
[[-method | ".SRUtil" and related classes |