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