(Legacy) Quality assessment summaries from MAQ map files
Construct objects indicating read or alignment quality
".SRUtil" and related classes
(Legacy) A base class for Roche experiment-wide data
Quality assessment of fastq files and ShortReadQ objects
(Legacy) "ExperimentPath" class representing a file hierarchy of data
files
(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base
classes for short read image intensities
Summarize nucleotide, amino acid, or quality scores by cycle
Deprecated functions from the ShortRead package
"SRFilterResult" for SRFilter output and statistics
Virtual class for representing quality assessment results
Classes "SolexaIntensity" and "SolexaIntensityInfo"
Quality scores for short reads and their alignments
"ShortRead" class for short reads
(Legacy) Read aligned reads and their quality scores into R representations
Renew (update) a ShortRead object with new values
Class "Snapshot"
(Legacy) Accessors for ShortRead classes
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
(Legacy) Read Solexa qseq files as fastq-style quality scores
"ShortReadQ" class for short reads and their quality scores
FASTQ input and manipulation.
(Legacy) Read short reads and their quality scores into R representations
Remove sequences with ambiguous nucleotides from short read classes
Summarize XStringSet read frequencies
(Legacy) Read Solexa prb files as fastq-style quality scores
(Legacy) Get a list of the sequences in a Maq .bfa file
(Legacy) "AlignedRead" class for aligned short reads
(Legacy) Construct objects of class "RtaIntensity"
Perform quality assessment on short reads
Efficiently calculate the sum of quality scores across bases
Deprecated and defunct functions
Summarize quality assessment results into a report
Functions for user-created and built-in ShortRead filters
(Legacy) Quality assessment summaries from Bowtie files
(Legacy) Class "RtaIntensity"
(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
(Updated) classes for representing quality assessment results
(Legacy) Roche (454) experiment-wide data container
(Legacy) Quality assessment summaries from Solexa export and
realign files
Summarize low-complexity sequences
Class "SnapshotFunction"
Read and write FASTQ-formatted files
Edit distances between reads and a small number of short references
Trim ends of reads based on nucleotides or qualities
Read and write FASTA files to or from ShortRead objects
(Legacy) AlignedDataFrame constructor
(Legacy) Construct objects of class "AlignedRead"
Class "SpTrellis"
Tools to visualize genomic data
(Updated) quality assessment reports on short reads
Read one or more columns into XStringSet (e.g., DNAStringSet) objects
Count lines in all (text) files in a directory whose file name
matches a pattern
Filter fastq from one file to another
Utilities for common, simple operations
Order, sort, and find duplicates in XStringSet objects
"SRFilter" for representing functions operating on ShortRead objects
(Legacy) Construct objects of class "SolexaIntensity" and
"SolexaIntensityInfo"
(Legacy) "SolexaPath" class representing a standard output file hierarchy
Sampling and streaming records from fastq files
(Legacy) Read Illumina image intensity files
(Legacy) "RochePath" class representing a Roche (454) experiment location