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 (DEFUNCT!)
DNAString-class         DNAString objects
GENETIC_CODE            The Standard Genetic Code and its known
                        variants
HNF4alpha               Known HNF4alpha binding sequences
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
InDel-class             InDel objects
MIndex-class            MIndex objects
MaskedXString-class     MaskedXString objects
MultipleAlignment-class
                        MultipleAlignment objects
PDict-class             PDict objects
PairwiseAlignments-class
                        PairwiseAlignments,
                        PairwiseAlignmentsSingleSubject, and
                        PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io   Write a PairwiseAlignments object to a file
QualityScaledXStringSet-class
                        QualityScaledBStringSet,
                        QualityScaledDNAStringSet,
                        QualityScaledRNAStringSet and
                        QualityScaledAAStringSet objects
RNAString-class         RNAString objects
XString-class           BString objects
XStringPartialMatches-class
                        XStringPartialMatches objects
XStringQuality-class    PhredQuality, SolexaQuality and IlluminaQuality
                        objects
XStringSet-class        XStringSet objects
XStringSet-comparison   Comparing and ordering the elements in one or
                        more XStringSet objects
XStringSet-io           Read/write an XStringSet object from/to a file
XStringSetList-class    XStringSetList objects
XStringViews-class      The XStringViews class
align-utils             Utility functions related to sequence alignment
chartr,ANY,ANY,XString-method
                        Translating letters of a sequence
detail                  Show (display) detailed object content
dinucleotideFrequencyTest
                        Pearson's chi-squared Test and G-tests for
                        String Position Dependence
findPalindromes         Searching a sequence for palindromes
getSeq                  getSeq
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'
lowlevel-matching       Low-level matching functions
maskMotif               Masking by content (or by position)
match-utils             Utility functions operating on the matches
                        returned by a high-level matching function
matchLRPatterns         Find paired matches in a sequence
matchPDict              Matching a dictionary of patterns against a
                        reference
matchPDict-inexact      Inexact matching with
                        matchPDict()/countPDict()/whichPDict()
matchPWM                PWM creating, matching, 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.
misc                    Some miscellaneous stuff
needwunsQS              (Deprecated) Needleman-Wunsch Global Alignment
oligonucleotideFrequency
                        Calculate the frequency of oligonucleotides in
                        a DNA or RNA sequence (and other related
                        functions)
padAndClip              Pad and clip strings
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
replaceAt               Extract/replace arbitrary substrings from/in a
                        string or set of strings.
replaceLetterAt         Replacing letters in a sequence (or set of
                        sequences) at some specified locations
reverseComplement       Sequence reversing and complementing
stringDist              String Distance/Alignment Score Matrix
substitution.matrices   Scoring matrices
toComplex               Turning a DNA sequence into a vector of complex
                        numbers
translate               Translating DNA/RNA sequences
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