This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
|Author||Martin Morgan, Michael Lawrence, Simon Anders|
|Date of publication||None|
|Maintainer||Bioconductor Package Maintainer <email@example.com>|
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 and write 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