AAString-class          AAString objects
align-utils             Utility functions related to sequence alignment
AlignedXStringSet-class
                        AlignedXStringSet and QualityAlignedXStringSet
                        objects
AMINO_ACID_CODE         The Single-Letter Amino Acid Code
chartr                  Replace letters in a sequence or set of
                        sequences
detail                  Show (display) detailed object content
dinucleotideFrequencyTest
                        Pearson's chi-squared Test and G-tests for
                        String Position Dependence
DNAString-class         DNAString objects
findPalindromes         Searching a sequence for palindromes
GENETIC_CODE            The Standard Genetic Code and its known
                        variants
getSeq                  getSeq
gregexpr2               A replacement for R standard gregexpr function
HNF4alpha               Known HNF4alpha binding sequences
InDel-class             InDel objects
injectHardMask          Injecting a hard mask in a sequence
IUPAC_CODE_MAP          The IUPAC Extended Genetic Alphabet
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
MaskedXString-class     MaskedXString objects
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
matchPattern            String searching functions
matchPDict              Matching a dictionary of patterns against a
                        reference
matchPDict-inexact      Inexact matching with
                        matchPDict()/countPDict()/whichPDict()
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.
matchPWM                PWM creating, matching, and related utilities
MIndex-class            MIndex objects
misc                    Some miscellaneous stuff
MultipleAlignment-class
                        MultipleAlignment objects
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
PairwiseAlignments-class
                        PairwiseAlignments,
                        PairwiseAlignmentsSingleSubject, and
                        PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io   Write a PairwiseAlignments object to a file
PDict-class             PDict objects
phiX174Phage            Versions of bacteriophage phiX174 complete
                        genome and sample short reads
pid                     Percent Sequence Identity
pmatchPattern           Longest Common Prefix/Suffix/Substring
                        searching functions
QualityScaledXStringSet-class
                        QualityScaledBStringSet,
                        QualityScaledDNAStringSet,
                        QualityScaledRNAStringSet and
                        QualityScaledAAStringSet objects
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
RNAString-class         RNAString objects
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
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
yeastSEQCHR1            An annotation data file for CHR1 in the
                        yeastSEQ package
