| 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 |
(Legacy) "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 |
| QualityScore-class |
Quality scores for short reads and their alignments |
| qualPath |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| rbind-method |
Virtual class for representing quality assessment results |
| rbind-method |
(Updated) quality assessment reports on short reads |
| read454 |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| read454-method |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readAligned |
(Legacy) Read aligned reads and their quality scores into R representations |
| readAligned-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readAligned-method |
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations |
| readAligned-method |
Deprecated and defunct functions |
| readAligned-method |
(Legacy) Read aligned reads and their quality scores into R representations |
| readBaseQuality |
(Legacy) Read short reads and their quality scores into R representations |
| readBaseQuality-method |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readBaseQuality-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readBaseQuality-method |
(Legacy) Read short reads and their quality scores into R representations |
| readBfaToc |
(Legacy) Get a list of the sequences in a Maq .bfa file |
| readCount |
(Legacy) A base class for Roche experiment-wide data |
| readData |
(Legacy) A base class for Roche experiment-wide data |
| reader |
Class "SnapshotFunction" |
| readFasta |
Read and write FASTA files to or from ShortRead objects |
| readFasta-method |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readFasta-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readFasta-method |
Read and write FASTA files to or from ShortRead objects |
| readFastaQual |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readFastaQual-method |
(Legacy) "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 |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readFastq-method |
Read and write FASTQ-formatted files |
| readIndex |
(Legacy) A base class for Roche experiment-wide data |
| readIntensities |
(Legacy) Read Illumina image intensity files |
| readIntensities-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readIntensities-method |
(Legacy) Read Illumina image intensity files |
| readIntensityInfo |
(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
| readPath |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readPrb |
(Legacy) Read Solexa prb files as fastq-style quality scores |
| readPrb-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readPrb-method |
(Legacy) Read Solexa prb files as fastq-style quality scores |
| readQseq |
(Legacy) Read Solexa qseq files as fastq-style quality scores |
| readQseq-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| readQseq-method |
(Legacy) Read Solexa qseq files as fastq-style quality scores |
| readQual |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| readQual-method |
(Legacy) "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 |
(Legacy) Quality assessment summaries from Bowtie files |
| report-method |
Quality assessment of fastq files and ShortReadQ objects |
| report-method |
(Legacy) Quality assessment summaries from MAQ map files |
| report-method |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| report-method |
(Legacy) "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 |
(Legacy) Quality assessment summaries from Bowtie files |
| report_html-method |
Quality assessment of fastq files and ShortReadQ objects |
| report_html-method |
(Legacy) Quality assessment summaries from MAQ map files |
| report_html-method |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| restore |
Class "SpTrellis" |
| restore-method |
Class "SpTrellis" |
| reverse-method |
Quality scores for short reads and their alignments |
| reverse-method |
"ShortReadQ" class for short reads and their quality scores |
| reverseComplement-method |
"ShortReadQ" class for short reads and their quality scores |
| right |
Class "SpTrellis" |
| right-method |
Class "SpTrellis" |
| RochePath |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| RochePath-class |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| RocheSet |
(Legacy) Roche (454) experiment-wide data container |
| RocheSet-class |
(Legacy) Roche (454) experiment-wide data container |
| RocheSet-method |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| RtaIntensity |
(Legacy) Construct objects of class "RtaIntensity" |
| RtaIntensity-class |
(Legacy) Class "RtaIntensity" |
| runNames |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| runNames-method |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| sapply-method |
".SRUtil" and related classes |
| scanPath |
(Legacy) 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 |
(Legacy) "AlignedRead" class for aligned short reads |
| show-method |
(Legacy) "ExperimentPath" class representing a file hierarchy of data files |
| show-method |
(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities |
| show-method |
Quality scores for short reads and their alignments |
| show-method |
(Legacy) "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 |
(Legacy) A base class for Roche experiment-wide data |
| show-method |
".SRUtil" and related classes |
| show-method |
"ShortRead" class for short reads |
| show-method |
FASTQ input and manipulation. |
| show-method |
Class '"Snapshot"' |
| show-method |
Class "SnapshotFunction" |
| show-method |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| show-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| show-method |
(Legacy) "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 |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| SolexaExportQA-class |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| SolexaIntensity |
(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo" |
| SolexaIntensity-class |
Classes "SolexaIntensity" and "SolexaIntensityInfo" |
| SolexaIntensityInfo |
(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo" |
| SolexaIntensityInfo-class |
Classes "SolexaIntensity" and "SolexaIntensityInfo" |
| SolexaPath |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| solexaPath |
(Legacy) Accessors for ShortRead classes |
| SolexaPath-class |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| SolexaRealignQA-class |
(Legacy) Quality assessment summaries from Solexa export and realign files |
| SolexaSet |
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations |
| SolexaSet-class |
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations |
| SolexaSet-method |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| SolexaSet-method |
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations |
| sourcePath |
(Legacy) A base class for Roche experiment-wide data |
| SpTrellis |
Class "SpTrellis" |
| SpTrellis-class |
Class "SpTrellis" |
| spViewPerFeature |
Tools to visualize genomic data |
| srapply |
Deprecated and defunct functions |
| 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 |
(Legacy) "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 |
"ShortRead" class for short reads |
| sread-method |
"ShortRead" class for short reads |
| 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 |
".SRUtil" and related classes |
| SRList-class |
".SRUtil" and related classes |
| srorder |
Order, sort, and find duplicates in XStringSet objects |
| srorder-method |
(Legacy) "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 |
(Legacy) "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 |
(Legacy) 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 |
(Legacy) "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 |
(Legacy) "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 |
FASTQ input and manipulation. |
| .ShortReadBase-class |
FASTQ input and manipulation. |
| .Solexa-class |
FASTQ input and manipulation. |
| .SRUtil-class |
".SRUtil" and related classes |
| [-method |
(Legacy) "AlignedRead" class for aligned short reads |
| [-method |
(Legacy) "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 |
"ShortReadQ" class for short reads and their quality scores |
| [[-method |
(Legacy) "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 |