.QA-class               Virtual class for representing quality
                        assessment results
.SRUtil-class           ".SRUtil" and related classes
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
BAMQA-class             Quality assessment from BAM files
BowtieQA-class          Quality assessment summaries from Bowtie files
ExperimentPath-class    "ExperimentPath" class representing a file
                        hierarchy of data files
FastqFile-class         Sampling and streaming records from fastq files
FastqQA                 Quality assessment of fastq files and
                        ShortReadQ objects
GappedReads-class       GappedReads objects
Intensity-class         "Intensity", "IntensityInfo", and
                        "IntensityMeasure" base classes for short read
                        image intensities
MAQMapQA-class          Quality assessment summaries from MAQ map files
NumericQuality          Construct objects indicating read or alignment
                        quality
QA-class                (Updated) classes for representing quality
                        assessment results
QualityScore-class      Quality scores for short reads and their
                        alignments
RochePath-class         "RochePath" class representing a Roche (454)
                        experiment location
RocheSet-class          Roche (454) experiment-wide data container
RtaIntensity            Construct objects of class "RtaIntensity"
RtaIntensity-class      Class "RtaIntensity"
SRFilter-class          "SRFilter" for representing functions operating
                        on ShortRead objects
SRFilterResult-class    "SRFilterResult" for SRFilter output and
                        statistics
SRSet-class             A base class for Roche experiment-wide data
ShortRead-class         "ShortRead" class for short reads
ShortReadBase-package   Base classes and methods for high-throughput
                        short-read sequencing data.
ShortReadQ-class        "ShortReadQ" class for short reads and their
                        quality scores
Snapshot-class          Class '"Snapshot"'
SnapshotFunction-class
                        Class "SnapshotFunction"
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"
SolexaPath-class        "SolexaPath" class representing a standard
                        output file hierarchy
SolexaSet-class         "SolexaSet" coordinating Solexa output
                        locations with sample annotations
SpTrellis-class         Class "SpTrellis"
accessors               Accessors for ShortRead classes
alphabetByCycle         Summarize short read nucleotide or quality
                        scores by cycle
alphabetScore           Efficiently calculate the sum of quality scores
                        across bases
clean                   Remove sequences with ambiguous nucleotides
                        from short read classes
countLines              Count lines in all (text) files in a directory
                        whose file name matches a pattern
deprecated              Deprecated and defunct functions
dustyScore              Summarize low-complexity sequences
polyn                   Utilities for common, simple operations
qa                      Perform quality assessment on short reads
qa2                     (Updated) quality assessment reports on short
                        reads
readAligned             Read aligned reads and their quality scores
                        into R representations
readBaseQuality         Read short reads and their quality scores into
                        R representations
readBfaToc              Get a list of the sequences in a Maq .bfa file
readFasta               Read and write FASTA files to or from ShortRead
                        objects
readFastq               Read and write FASTQ-formatted files
readIntensities         Read Illumina image intensity files
readPrb                 Read Solexa prb files as fastq-style quality
                        scores
readQseq                Read Solexa qseq files as fastq-style quality
                        scores
readXStringColumns      Read one or more columns into XStringSet (e.g.,
                        DNAStringSet) objects
renewable               Renew (update) a ShortRead object with new
                        values
report                  Summarize quality assessment results into a
                        report
spViewPerFeature        Tools to visualize genomic data
srFilter                Functions for user-created and built-in
                        ShortRead filters
srapply                 Apply-like function for distribution across
                        MPI-based clusters.
srdistance              Edit distances between reads and a small number
                        of short references
srduplicated            Order, sort, and find duplicates in XStringSet
                        objects
tables                  Summarize XStringSet read frequencies
trimTails               Trim ends of reads based on nucleotides or
                        qualities
uniqueFilter            Deprecated functions from the ShortRead package
