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A B C D E F I L M N O P Q R S T U V W Y misc
| ShortReadBase-package | Base classes and methods for high-throughput short-read sequencing |
| %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 |
| .ShortReadBase-class | Base classes and methods for high-throughput short-read sequencing |
| .Solexa-class | Base classes and methods for high-throughput short-read sequencing |
| .SRUtil-class | ".SRUtil" and related classes |
| 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 |
| 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 |
| append-method | "ShortReadQ" class for short reads and their quality scores |
| ArrayIntensity | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| ArrayIntensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| 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 |
| chromosome | Accessors for ShortRead classes |
| chromosome-method | "AlignedRead" class for aligned short reads |
| chromosomeFilter | Functions for user-created and built-in ShortRead filters |
| 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 |
| coerce-method | "AlignedRead" class for aligned short reads |
| coerce-method | Quality scores for short reads and their alignments |
| coerce-method | "ShortReadQ" class for short reads and their quality scores |
| compact-method | Quality scores for short reads and their alignments |
| compact-method | "ShortRead" class for short reads |
| compact-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 |
| coverage-method | "AlignedRead" class for aligned short reads |
| dataPath | Accessors for ShortRead classes |
| 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 |
| dim-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| 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 |
| 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 records from fastq files |
| FastqSampler-class | Sampling records from fastq files |
| id | Accessors for ShortRead classes |
| id-method | "ShortRead" class for short reads |
| idFilter | Functions for user-created and built-in ShortRead filters |
| 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 |
| Intensity-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| IntensityInfo-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| IntensityMeasure-class | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| laneDescription | Accessors for ShortRead classes |
| laneNames | Accessors for ShortRead classes |
| laneNames-method | "SolexaSet" coordinating Solexa output locations with sample |
| lapply-method | ".SRUtil" and related classes |
| length-method | Quality scores for short reads and their alignments |
| length-method | ".SRUtil" and related classes |
| length-method | "ShortRead" class for short reads |
| 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 |
| name | "SRFilter" for representing functions operating on ShortRead objects |
| name-method | "SRFilter" for representing functions operating on ShortRead objects |
| names-method | ".SRUtil" and related classes |
| names<--method | ".SRUtil" and related classes |
| 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 |
| 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 | Perform quality assessment on short reads |
| 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 |
| QualityScore-class | Quality scores for short reads and their alignments |
| qualPath | "RochePath" class representing a Roche (454) experiment location |
| 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 |
| 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 |
| 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 | "SolexaPath" class representing a standard output file hierarchy |
| readFastq-method | Read and write FASTQ-formatted files |
| readIndex | A base class for Roche experiment-wide data |
| readInfo | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| 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 |
| 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 |
| Sampler-class | Sampling records from fastq files |
| 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 |
| 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 |
| 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 | A base class for Roche experiment-wide data |
| show-method | ".SRUtil" and related classes |
| show-method | Sampling records from fastq files |
| show-method | "ShortRead" class for short reads |
| show-method | Base classes and methods for high-throughput short-read sequencing |
| 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 |
| 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 |
| SolexaSet-class | "SolexaSet" coordinating Solexa output locations with sample |
| SolexaSet-method | "SolexaPath" class representing a standard output file hierarchy |
| SolexaSet-method | "SolexaSet" coordinating Solexa output locations with sample |
| sourcePath | A base class for Roche experiment-wide 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 |
| 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 |
| 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 |
| trimLRPatterns-method | "ShortRead" class for short reads |
| uniqueFilter | Deprecated functions from the ShortRead package |
| vclass | Accessors for ShortRead classes |
| 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 |
| writeFastq | Read and write FASTQ-formatted files |
| writeFastq-method | "ShortReadQ" class for short reads and their quality scores |
| yield | Sampling records from fastq files |
| yield-method | Sampling records from fastq files |
| [-method | "AlignedRead" class for aligned short reads |
| [-method | "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for |
| [-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 |
| [[-method | Quality scores for short reads and their alignments |
| [[-method | ".SRUtil" and related classes |