The Standard Genetic Code and its known variants
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
PhredQuality, SolexaQuality and IlluminaQuality objects
Comparing and ordering the elements in one or more XStringSet objects
Read/write an XStringSet object from/to a file
Replace letters in a sequence or set of sequences
Pearson's chi-squared Test and G-tests for String Position Dependence
A replacement for R standard gregexpr function
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
Obtain the length of the longest substring containing only 'letter'
Utility functions operating on the matches returned by a high-level matching function
Matching a dictionary of patterns against a reference
PWM creating, matching, and related utilities
Find "theoretical amplicons" mapped to a probe pair
(Deprecated) A function to match a query sequence to the sequences of a set of probes.
Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
Longest Common Prefix/Suffix/Substring searching functions
Extract/replace arbitrary substrings from/in a string or set of strings.
Replacing letters in a sequence (or set of sequences) at some specified locations
seqinfo() method for DNAStringSet objects
Turning a DNA sequence into a vector of complex numbers
Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
An annotation data file for CHR1 in the yeastSEQ package