rbind-method |
Virtual class for representing quality assessment results |
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 |
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 |
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 |
Virtual class for representing quality assessment results |
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" |
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 |
!-method |
"SRFilterResult" for SRFilter output and statistics |
%in%-method |
"AlignedRead" class for aligned short reads |
.QA-class |
Virtual class 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 |