AAString-class          AAString objects
AMINO_ACID_CODE         The Single-Letter Amino Acid Code
AlignedXStringSet-class
                        AlignedXStringSet and QualityAlignedXStringSet
                        objects
BOC_SubjectString-class
                        BOC\_SubjectString and BOC2\_SubjectString
                        objects
DNAString-class         DNAString objects
GENETIC_CODE            The Standard Genetic Code
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
InDel-class             InDel objects
MIndex-class            MIndex objects
MaskedXString-class     MaskedXString objects
PDict-class             PDict objects
PairwiseAlignedXStringSet-class
                        PairwiseAlignedXStringSet,
                        PairwiseAlignedFixedSubject, and
                        PairwiseAlignedFixedSubjectSummary objects
QualityScaledXStringSet-class
                        QualityScaledBStringSet,
                        QualityScaledDNAStringSet,
                        QualityScaledRNAStringSet and
                        QualityScaledAAStringSet objects
RNAString-class         RNAString objects
XString-class           BString objects
XStringPartialMatches-class
                        XStringPartialMatches objects
XStringQuality-class    PhredQuality and SolexaQuality objects
XStringSet-class        BStringSet, DNAStringSet, RNAStringSet and
                        AAStringSet objects
XStringViews-class      The XStringViews class
XStringViews-constructors
                        Basic functions for creating or modifying
                        XStringViews objects
align-utils             Utility functions related to sequence alignment
basecontent             Obtain the ATCG content of a gene
chartr,ANY,ANY,XString-method
                        Translating letters of a sequence
complementSeq           Complementary sequence.
findPalindromes         Searching a sequence for palindromes or
                        complemented palindromes
gregexpr2               A replacement for R standard gregexpr function
injectHardMask          Injecting a hard mask in a sequence
letter                  Subsetting a string
letterFrequency         Calculate the frequency of letters in a
                        biological sequence, or the consensus matrix of
                        a set of sequences
longestConsecutive      Obtain the length of the longest substring
                        containing only 'letter'
maskMotif               Masking by content (or by position)
match-utils             Utility functions related to pattern matching
matchLRPatterns         Find paired matches in a sequence
matchPDict              Searching a sequence for patterns stored in a
                        preprocessed dictionary
matchPDict-inexact      Inexact matching with
                        matchPDict()/countPDict()/whichPDict()
matchPWM                A simple PWM matching function and related
                        utilities
matchPattern            String searching functions
matchProbePair          Find "theoretical amplicons" mapped to a probe
                        pair
matchprobes             A function to match a query sequence to the
                        sequences of a set of probes.
needwunsQS              (Deprecated) Needleman-Wunsch Global Alignment
oligonucleotideFrequency
                        Calculate the frequency of oligonucleotides in
                        a DNA or RNA sequence, plus some related
                        functions
pairwiseAlignment       Optimal Pairwise Alignment
phiX174Phage            Versions of bacteriophage phiX174 complete
                        genome and sample short reads
pid                     Percent Sequence Identity
pmatchPattern           Longest Common Prefix/Suffix/Substring
                        searching functions
read.XStringViews       Read/write an XStringSet or XStringViews object
                        from/to a file
readFASTA               Functions to read/write FASTA formatted files
replaceLetterAt         Replacing letters in a sequence (or set of
                        sequences) at some specified locations
reverseComplement       Sequence reversing and complementing
reverseSeq              Reverse Sequence
stringDist              String Distance/Alignment Score Matrix
subXString              Fast substring extraction
substitution.matrices   Scoring matrices
toComplex               Turning a DNA sequence into a vector of complex
                        numbers
translate               DNA/RNA transcription and translation
trimLRPatterns          Trim Flanking Patterns from Sequences
xscat                   Concatenate sequences contained in XString,
                        XStringSet and/or XStringViews objects
yeastSEQCHR1            An annotation data file for CHR1 in the
                        yeastSEQ package
