| 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, write, and count records in 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 |
