String objects representing biological sequences, and matching algorithms

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Documentation for package ‘Biostrings’ version 2.10.22

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A B C D E F G H I L M N O P Q R S T U V W X Y misc

!=,BString,character-method BString objects
!=,character,BString-method BString objects
!=,character,XStringViews-method The XStringViews class
!=,XString,XString-method BString objects
!=,XString,XStringViews-method The XStringViews class
!=,XStringViews,character-method The XStringViews class
!=,XStringViews,XString-method The XStringViews class
!=,XStringViews,XStringViews-method The XStringViews class
.inplaceReplaceLetterAt Replacing letters in a sequence at some specified locations
==,BString,character-method BString objects
==,character,BString-method BString objects
==,character,XStringViews-method The XStringViews class
==,XString,XString-method BString objects
==,XString,XStringViews-method The XStringViews class
==,XStringViews,character-method The XStringViews class
==,XStringViews,XString-method The XStringViews class
==,XStringViews,XStringViews-method The XStringViews class

-- A --

AAString AAString objects
AAString-class AAString objects
AAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AA_ALPHABET AAString objects
ACtree PDict objects
ACtree-class PDict objects
ACtree2 PDict objects
ACtree2-class PDict objects
adjacentViews Basic functions for creating or modifying XStringViews objects
align-utils Utility functions related to sequence alignment
aligned AlignedXStringSet and QualityAlignedXStringSet objects
aligned,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
aligned,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
AlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
alignScore (Deprecated) Needleman-Wunsch Global Alignment
alphabet BString objects
alphabet,AAString-method AAString objects
alphabet,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
alphabet,BString-method BString objects
alphabet,DNAString-method DNAString objects
alphabet,MaskedXString-method MaskedXString objects
alphabet,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
alphabet,RNAString-method RNAString objects
alphabet,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
alphabet,XStringViews-method The XStringViews class
alphabetFrequency Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,DNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,DNAStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,MaskedXString-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,RNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,RNAStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,XString-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,XStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
alphabetFrequency,XStringViews-method Function to calculate the frequency of letters in a biological sequence and related functions
AMINO_ACID_CODE The Single-Letter Amino Acid Code
append,QualityScaledXStringSet,QualityScaledXStringSet-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
append,XStringSet,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.character,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
as.character,MaskedXString-method MaskedXString objects
as.character,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
as.character,XString-method BString objects
as.character,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.character,XStringViews-method The XStringViews class
as.complex,DNAString-method Turning a DNA sequence into a vector of complex numbers
as.integer,PhredQuality-method PhredQuality and SolexaQuality objects
as.integer,SolexaQuality-method PhredQuality and SolexaQuality objects
as.list,MTB_PDict-method PDict objects
as.matrix,ACtree-method PDict objects
as.matrix,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
as.matrix,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.matrix,XStringViews-method The XStringViews class
as.numeric,PhredQuality-method PhredQuality and SolexaQuality objects
as.numeric,SolexaQuality-method PhredQuality and SolexaQuality objects

-- B --

BLOSUM100 Scoring matrices
BLOSUM45 Scoring matrices
BLOSUM50 Scoring matrices
BLOSUM62 Scoring matrices
BLOSUM80 Scoring matrices
BOC2_SubjectString BOC_SubjectString and BOC2_SubjectString objects
BOC2_SubjectString-class BOC_SubjectString and BOC2_SubjectString objects
BOC_SubjectString BOC_SubjectString and BOC2_SubjectString objects
BOC_SubjectString-class BOC_SubjectString and BOC2_SubjectString objects
BString BString objects
BString-class BString objects
BStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringViews Basic functions for creating or modifying XStringViews objects
BStringViews,ANY-method Basic functions for creating or modifying XStringViews objects
BStringViews,file-method Basic functions for creating or modifying XStringViews objects
BStringViews,XString-method Basic functions for creating or modifying XStringViews objects
BStringViews,XStringViews-method Basic functions for creating or modifying XStringViews objects
ByPos_MIndex-class MIndex objects

-- C --

cDNA DNA/RNA transcription and translation
CharacterToFASTArecords Read/write an XStringSet or XStringViews object from/to a file
chartr Translating letters of a sequence
chartr,MaskedXString-method Translating letters of a sequence
chartr,XString-method Translating letters of a sequence
chartr,XStringSet-method Translating letters of a sequence
chartr,XStringViews-method Translating letters of a sequence
class:AAString AAString objects
class:AAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ACtree PDict objects
class:ACtree2 PDict objects
class:AlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
class:BOC2_SubjectString BOC_SubjectString and BOC2_SubjectString objects
class:BOC_SubjectString BOC_SubjectString and BOC2_SubjectString objects
class:BString BString objects
class:BStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ByPos_MIndex MIndex objects
class:DNAString DNAString objects
class:DNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:InDel InDel objects
class:MaskedAAString MaskedXString objects
class:MaskedBString MaskedXString objects
class:MaskedDNAString MaskedXString objects
class:MaskedRNAString MaskedXString objects
class:MaskedXString MaskedXString objects
class:MIndex MIndex objects
class:MTB_PDict PDict objects
class:PairwiseAlignedFixedSubject PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
class:PairwiseAlignedFixedSubjectSummary PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
class:PDict PDict objects
class:PDict3Parts PDict objects
class:PhredQuality PhredQuality and SolexaQuality objects
class:PreprocessedTB PDict objects
class:QualityAlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
class:QualityScaledAAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledBStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledDNAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledRNAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledXStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:RNAString RNAString objects
class:RNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:SolexaQuality PhredQuality and SolexaQuality objects
class:TB_PDict PDict objects
class:Twobit PDict objects
class:XString BString objects
class:XStringPartialMatches XStringPartialMatches objects
class:XStringQuality PhredQuality and SolexaQuality objects
class:XStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:XStringViews The XStringViews class
codons DNA/RNA transcription and translation
codons,DNAString-method DNA/RNA transcription and translation
codons,MaskedDNAString-method DNA/RNA transcription and translation
codons,MaskedRNAString-method DNA/RNA transcription and translation
codons,RNAString-method DNA/RNA transcription and translation
coerce,AAString,MaskedAAString-method MaskedXString objects
coerce,BString,MaskedBString-method MaskedXString objects
coerce,BString,PhredQuality-method PhredQuality and SolexaQuality objects
coerce,BString,SolexaQuality-method PhredQuality and SolexaQuality objects
coerce,BStringSet,PhredQuality-method PhredQuality and SolexaQuality objects
coerce,BStringSet,SolexaQuality-method PhredQuality and SolexaQuality objects
coerce,character,PhredQuality-method PhredQuality and SolexaQuality objects
coerce,character,SolexaQuality-method PhredQuality and SolexaQuality objects
coerce,DNAString,MaskedDNAString-method MaskedXString objects
coerce,integer,PhredQuality-method PhredQuality and SolexaQuality objects
coerce,integer,SolexaQuality-method PhredQuality and SolexaQuality objects
coerce,MaskedAAString,AAString-method MaskedXString objects
coerce,MaskedBString,BString-method MaskedXString objects
coerce,MaskedDNAString,DNAString-method MaskedXString objects
coerce,MaskedRNAString,RNAString-method MaskedXString objects
coerce,MaskedXString,MaskCollection-method MaskedXString objects
coerce,MaskedXString,NormalIRanges-method MaskedXString objects
coerce,MaskedXString,XStringViews-method MaskedXString objects
coerce,numeric,PhredQuality-method PhredQuality and SolexaQuality objects
coerce,numeric,SolexaQuality-method PhredQuality and SolexaQuality objects
coerce,PhredQuality,integer-method PhredQuality and SolexaQuality objects
coerce,PhredQuality,numeric-method PhredQuality and SolexaQuality objects
coerce,RNAString,MaskedRNAString-method MaskedXString objects
coerce,SolexaQuality,integer-method PhredQuality and SolexaQuality objects
coerce,SolexaQuality,numeric-method PhredQuality and SolexaQuality objects
coerce,XStringSet,AAStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
coerce,XStringSet,BStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
coerce,XStringSet,DNAStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
coerce,XStringSet,RNAStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
compareStrings Utility functions related to sequence alignment
compareStrings,AlignedXStringSet,AlignedXStringSet-method Utility functions related to sequence alignment
compareStrings,character,character-method Utility functions related to sequence alignment
compareStrings,PairwiseAlignedFixedSubject,missing-method Utility functions related to sequence alignment
compareStrings,XString,XString-method Utility functions related to sequence alignment
compareStrings,XStringSet,XStringSet-method Utility functions related to sequence alignment
complement Sequence reversing and complementing
complement,DNAString-method Sequence reversing and complementing
complement,DNAStringSet-method Sequence reversing and complementing
complement,MaskedDNAString-method Sequence reversing and complementing
complement,MaskedRNAString-method Sequence reversing and complementing
complement,RNAString-method Sequence reversing and complementing
complement,RNAStringSet-method Sequence reversing and complementing
complement,XStringViews-method Sequence reversing and complementing
complementedPalindromeArmLength Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,DNAString-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,XStringViews-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,DNAString-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,XStringViews-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,DNAString-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,XStringViews-method Searching a sequence for palindromes or complemented palindromes
consensusMatrix Utility functions related to sequence alignment
consensusMatrix,character-method Utility functions related to sequence alignment
consensusMatrix,list-method Utility functions related to sequence alignment
consensusMatrix,matrix-method Utility functions related to sequence alignment
consensusMatrix,PairwiseAlignedFixedSubject-method Utility functions related to sequence alignment
consensusMatrix,XStringSet-method Utility functions related to sequence alignment
consensusMatrix,XStringViews-method Utility functions related to sequence alignment
consensusString Utility functions related to sequence alignment
consensusString,ANY-method Utility functions related to sequence alignment
consmat Utility functions related to sequence alignment
consmat,ANY-method Utility functions related to sequence alignment
countIndex MIndex objects
countIndex,ByPos_MIndex-method MIndex objects
countIndex,MIndex-method MIndex objects
countPattern String searching functions
countPattern,BOC2_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
countPattern,character-method String searching functions
countPattern,MaskedXString-method String searching functions
countPattern,XString-method String searching functions
countPattern,XStringSet-method String searching functions
countPattern,XStringViews-method String searching functions
countPDict Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,MaskedXString-method Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XString-method Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XStringSet-method Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XStringViews-method Searching a sequence for patterns stored in a preprocessed dictionary
countPWM A simple PWM matching function and related utilities
coverage,AlignedXStringSet-method Utility functions related to sequence alignment
coverage,MaskedXString-method Utility functions related to pattern matching
coverage,MIndex-method Utility functions related to pattern matching
coverage,PairwiseAlignedFixedSubject-method Utility functions related to sequence alignment
coverage,PairwiseAlignedFixedSubjectSummary-method Utility functions related to sequence alignment
coverage,XStringViews-method Utility functions related to pattern matching

-- D --

deletion InDel objects
deletion,InDel-method InDel objects
dinucleotideFrequency Function to calculate the frequency of letters in a biological sequence and related functions
dna2rna DNA/RNA transcription and translation
DNAString DNAString objects
DNAString-class DNAString objects
DNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNA_ALPHABET DNAString objects
DNA_BASES DNAString objects
duplicated,PDict-method PDict objects
duplicated,PreprocessedTB-method PDict objects

-- E --

end,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
endIndex MIndex objects
endIndex,ByPos_MIndex-method MIndex objects
errorSubstitutionMatrices Scoring matrices
extractAllMatches Searching a sequence for patterns stored in a preprocessed dictionary

-- F --

fasta.info Functions to read/write FASTA formatted files
FASTArecordsToBStringViews Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToCharacter Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToXStringViews Read/write an XStringSet or XStringViews object from/to a file
findComplementedPalindromes Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,DNAString-method Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,MaskedXString-method Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,XStringViews-method Searching a sequence for palindromes or complemented palindromes
findPalindromes Searching a sequence for palindromes or complemented palindromes
findPalindromes,MaskedXString-method Searching a sequence for palindromes or complemented palindromes
findPalindromes,XString-method Searching a sequence for palindromes or complemented palindromes
findPalindromes,XStringViews-method Searching a sequence for palindromes or complemented palindromes

-- G --

gaps,MaskedXString-method MaskedXString objects
GENETIC_CODE The Standard Genetic Code
gregexpr2 A replacement for R standard gregexpr function

-- H --

hasOnlyBaseLetters Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,DNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,DNAStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,MaskedDNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,MaskedRNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,RNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,RNAStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
hasOnlyBaseLetters,XStringViews-method Function to calculate the frequency of letters in a biological sequence and related functions
head,PDict3Parts-method PDict objects
head,TB_PDict-method PDict objects

-- I --

InDel InDel objects
indel AlignedXStringSet and QualityAlignedXStringSet objects
indel,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
InDel-class InDel objects
initialize,ACtree-method PDict objects
initialize,ACtree2-method PDict objects
initialize,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
initialize,BOC2_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
initialize,BOC_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
initialize,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
initialize,PreprocessedTB-method PDict objects
initialize,QualityAlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
initialize,Twobit-method PDict objects
injectHardMask Injecting a hard mask in a sequence
injectHardMask,MaskedXString-method Injecting a hard mask in a sequence
injectHardMask,XStringViews-method Injecting a hard mask in a sequence
insertion InDel objects
insertion,InDel-method InDel objects
isMatching Utility functions related to pattern matching
isMatchingAt Utility functions related to pattern matching
isMatchingEndingAt Utility functions related to pattern matching
isMatchingEndingAt,character-method Utility functions related to pattern matching
isMatchingEndingAt,XString-method Utility functions related to pattern matching
isMatchingStartingAt Utility functions related to pattern matching
isMatchingStartingAt,character-method Utility functions related to pattern matching
isMatchingStartingAt,XString-method Utility functions related to pattern matching
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet

-- L --

lcprefix Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,character-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,XString-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,XString-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,XString-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,XString-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,XString-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,character-method Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,XString-method Longest Common Prefix/Suffix/Substring searching functions
length,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
length,MaskedXString-method MaskedXString objects
length,MIndex-method MIndex objects
length,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
length,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
length,PDict-method PDict objects
length,PDict3Parts-method PDict objects
length,PreprocessedTB-method PDict objects
length,XString-method BString objects
length,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
letter Subsetting a string
letter,character-method Subsetting a string
letter,MaskedXString-method Subsetting a string
letter,XString-method Subsetting a string
letter,XStringViews-method Subsetting a string

-- M --

mask Masking by content (or by position)
MaskedAAString MaskedXString objects
MaskedAAString-class MaskedXString objects
MaskedBString MaskedXString objects
MaskedBString-class MaskedXString objects
MaskedDNAString MaskedXString objects
MaskedDNAString-class MaskedXString objects
maskedratio,MaskedXString-method MaskedXString objects
MaskedRNAString MaskedXString objects
MaskedRNAString-class MaskedXString objects
maskedwidth,MaskedXString-method MaskedXString objects
MaskedXString MaskedXString objects
MaskedXString-class MaskedXString objects
maskMotif Masking by content (or by position)
maskMotif,MaskedXString,character-method Masking by content (or by position)
maskMotif,MaskedXString,XString-method Masking by content (or by position)
maskMotif,XString,ANY-method Masking by content (or by position)
masks MaskedXString objects
masks,MaskedXString-method MaskedXString objects
masks,XString-method MaskedXString objects
masks<-,MaskedXString,MaskCollection-method MaskedXString objects
masks<-,MaskedXString,NULL-method MaskedXString objects
masks<-,XString,ANY-method MaskedXString objects
masks<-,XString,NULL-method MaskedXString objects
match-utils Utility functions related to pattern matching
matchDNAPattern String searching functions
matchLRPatterns Find paired matches in a sequence
matchLRPatterns,MaskedXString-method Find paired matches in a sequence
matchLRPatterns,XString-method Find paired matches in a sequence
matchLRPatterns,XStringViews-method Find paired matches in a sequence
matchPattern String searching functions
matchPattern,BOC2_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
matchPattern,BOC_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
matchPattern,character-method String searching functions
matchPattern,MaskedXString-method String searching functions
matchPattern,XString-method String searching functions
matchPattern,XStringSet-method String searching functions
matchPattern,XStringViews-method String searching functions
matchPDict Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,MaskedXString-method Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XString-method Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XStringSet-method Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XStringViews-method Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict-exact Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict-inexact Inexact matching with matchPDict()/countPDict()/whichPDict()
matchProbePair Find "theoretical amplicons" mapped to a probe pair
matchProbePair,DNAString-method Find "theoretical amplicons" mapped to a probe pair
matchProbePair,MaskedDNAString-method Find "theoretical amplicons" mapped to a probe pair
matchProbePair,XStringViews-method Find "theoretical amplicons" mapped to a probe pair
matchPWM A simple PWM matching function and related utilities
maxScore A simple PWM matching function and related utilities
maxWeights A simple PWM matching function and related utilities
mergeIUPACLetters The IUPAC Extended Genetic Alphabet
MIndex MIndex objects
MIndex-class MIndex objects
mismatch Utility functions related to pattern matching
mismatch,AlignedXStringSet,missing-method Utility functions related to sequence alignment
mismatch,ANY,XStringViews-method Utility functions related to pattern matching
mismatchSummary Utility functions related to sequence alignment
mismatchSummary,AlignedXStringSet-method Utility functions related to sequence alignment
mismatchSummary,PairwiseAlignedFixedSubject-method Utility functions related to sequence alignment
mismatchSummary,PairwiseAlignedFixedSubjectSummary-method Utility functions related to sequence alignment
mismatchSummary,QualityAlignedXStringSet-method Utility functions related to sequence alignment
mismatchTable Utility functions related to sequence alignment
mismatchTable,AlignedXStringSet-method Utility functions related to sequence alignment
mismatchTable,PairwiseAlignedFixedSubject-method Utility functions related to sequence alignment
mismatchTable,QualityAlignedXStringSet-method Utility functions related to sequence alignment
mkAllStrings Function to calculate the frequency of letters in a biological sequence and related functions
MTB_PDict PDict objects
MTB_PDict-class PDict objects

-- N --

names,MIndex-method MIndex objects
names,PDict-method PDict objects
names,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
names<-,MIndex-method MIndex objects
names<-,PDict-method PDict objects
names<-,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
narrow,QualityScaledXStringSet-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
narrow,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
nchar,MaskedXString-method MaskedXString objects
nchar,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
nchar,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
nchar,XString-method BString objects
nchar,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,XStringViews-method The XStringViews class
neditAt Utility functions related to pattern matching
neditEndingAt Utility functions related to pattern matching
neditEndingAt,character-method Utility functions related to pattern matching
neditEndingAt,XString-method Utility functions related to pattern matching
neditStartingAt Utility functions related to pattern matching
neditStartingAt,character-method Utility functions related to pattern matching
neditStartingAt,XString-method Utility functions related to pattern matching
needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,character-method (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,XString-method (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,character-method (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,XString-method (Deprecated) Needleman-Wunsch Global Alignment
nindel AlignedXStringSet and QualityAlignedXStringSet objects
nindel,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
nindel,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
nindel,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
nmatch Utility functions related to pattern matching
nmatch,ANY,XStringViews-method Utility functions related to pattern matching
nmatch,PairwiseAlignedFixedSubject,missing-method Utility functions related to sequence alignment
nmatch,PairwiseAlignedFixedSubjectSummary,missing-method Utility functions related to sequence alignment
nmismatch Utility functions related to pattern matching
nmismatch,AlignedXStringSet,missing-method Utility functions related to sequence alignment
nmismatch,ANY,XStringViews-method Utility functions related to pattern matching
nmismatch,PairwiseAlignedFixedSubject,missing-method Utility functions related to sequence alignment
nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method Utility functions related to sequence alignment
nmismatchEndingAt Utility functions related to pattern matching
nmismatchStartingAt Utility functions related to pattern matching
nucleotideSubstitutionMatrix Scoring matrices

-- O --

oligonucleotideFrequency Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideFrequency,DNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideFrequency,MaskedXString-method Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideFrequency,RNAString-method Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideFrequency,XStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideFrequency,XStringViews-method Function to calculate the frequency of letters in a biological sequence and related functions
oligonucleotideTransitions Function to calculate the frequency of letters in a biological sequence and related functions
order BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
order,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects

-- P --

PairwiseAlignedFixedSubject PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubject-class PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubjectSummary PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubjectSummary-class PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
pairwiseAlignment Optimal Pairwise Alignment
pairwiseAlignment,character,character-method Optimal Pairwise Alignment
pairwiseAlignment,character,QualityScaledXStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,character,XString-method Optimal Pairwise Alignment
pairwiseAlignment,character,XStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,QualityScaledXStringSet,character-method Optimal Pairwise Alignment
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,QualityScaledXStringSet,XString-method Optimal Pairwise Alignment
pairwiseAlignment,QualityScaledXStringSet,XStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,XString,character-method Optimal Pairwise Alignment
pairwiseAlignment,XString,QualityScaledXStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,XString,XString-method Optimal Pairwise Alignment
pairwiseAlignment,XString,XStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,XStringSet,character-method Optimal Pairwise Alignment
pairwiseAlignment,XStringSet,QualityScaledXStringSet-method Optimal Pairwise Alignment
pairwiseAlignment,XStringSet,XString-method Optimal Pairwise Alignment
pairwiseAlignment,XStringSet,XStringSet-method Optimal Pairwise Alignment
palindromeArmLength Searching a sequence for palindromes or complemented palindromes
palindromeArmLength,XString-method Searching a sequence for palindromes or complemented palindromes
palindromeArmLength,XStringViews-method Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm,XString-method Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm,XStringViews-method Searching a sequence for palindromes or complemented palindromes
palindromeRightArm Searching a sequence for palindromes or complemented palindromes
palindromeRightArm,XString-method Searching a sequence for palindromes or complemented palindromes
palindromeRightArm,XStringViews-method Searching a sequence for palindromes or complemented palindromes
PAM120 Scoring matrices
PAM250 Scoring matrices
PAM30 Scoring matrices
PAM40 Scoring matrices
PAM70 Scoring matrices
pattern XStringPartialMatches objects
pattern,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
pattern,XStringPartialMatches-method XStringPartialMatches objects
patternFrequency PDict objects
patternFrequency,PDict-method PDict objects
PDict PDict objects
PDict,AsIs-method PDict objects
PDict,character-method PDict objects
PDict,DNAStringSet-method PDict objects
PDict,XStringViews-method PDict objects
PDict-class PDict objects
PDict3Parts PDict objects
PDict3Parts-class PDict objects
phiX174Phage Versions of bacteriophage phiX174 complete genome and sample short reads
PhredQuality PhredQuality and SolexaQuality objects
PhredQuality-class PhredQuality and SolexaQuality objects
pid Percent Sequence Identity
pid,PairwiseAlignedFixedSubject-method Percent Sequence Identity
pmatchPattern Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,character-method Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,XString-method Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern,XStringViews-method Longest Common Prefix/Suffix/Substring searching functions
PreprocessedTB PDict objects
PreprocessedTB-class PDict objects
print.needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
PWMscore A simple PWM matching function and related utilities

-- Q --

quality QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
quality,QualityScaledXStringSet-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityAlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
QualityAlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
QualityScaledAAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledAAStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledBStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledBStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledDNAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledDNAStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledRNAStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledRNAStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledXStringSet QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledXStringSet-class QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
qualitySubstitutionMatrices Scoring matrices
quPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads

-- R --

read.AAStringSet Read/write an XStringSet or XStringViews object from/to a file
read.BStringSet Read/write an XStringSet or XStringViews object from/to a file
read.BStringViews Read/write an XStringSet or XStringViews object from/to a file
read.DNAStringSet Read/write an XStringSet or XStringViews object from/to a file
read.RNAStringSet Read/write an XStringSet or XStringViews object from/to a file
read.XStringViews Read/write an XStringSet or XStringViews object from/to a file
readFASTA Functions to read/write FASTA formatted files
reduce,MaskedXString-method MaskedXString objects
rep,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
rep,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
rep,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
replaceLetterAt Replacing letters in a sequence at some specified locations
replaceLetterAt,DNAString-method Replacing letters in a sequence at some specified locations
replaceLetterAtLoc Replacing letters in a sequence at some specified locations
reverse,MaskedXString-method Sequence reversing and complementing
reverse,XString-method Sequence reversing and complementing
reverse,XStringSet-method Sequence reversing and complementing
reverse,XStringViews-method Sequence reversing and complementing
reverseComplement Sequence reversing and complementing
reverseComplement,DNAString-method Sequence reversing and complementing
reverseComplement,DNAStringSet-method Sequence reversing and complementing
reverseComplement,MaskedDNAString-method Sequence reversing and complementing
reverseComplement,MaskedRNAString-method Sequence reversing and complementing
reverseComplement,matrix-method A simple PWM matching function and related utilities
reverseComplement,RNAString-method Sequence reversing and complementing
reverseComplement,RNAStringSet-method Sequence reversing and complementing
reverseComplement,XStringViews-method Sequence reversing and complementing
rna2dna DNA/RNA transcription and translation
RNAString RNAString objects
RNAString-class RNAString objects
RNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNA_ALPHABET RNAString objects
RNA_BASES RNAString objects
RNA_GENETIC_CODE The Standard Genetic Code

-- S --

score PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
score,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
score,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
show,ACtree-method PDict objects
show,ACtree2-method PDict objects
show,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
show,ByPos_MIndex-method MIndex objects
show,MaskedXString-method MaskedXString objects
show,MTB_PDict-method PDict objects
show,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
show,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
show,QualityScaledXStringSet-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
show,TB_PDict-method PDict objects
show,Twobit-method PDict objects
show,XString-method BString objects
show,XStringPartialMatches-method XStringPartialMatches objects
show,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
show,XStringViews-method The XStringViews class
SolexaQuality PhredQuality and SolexaQuality objects
SolexaQuality-class PhredQuality and SolexaQuality objects
sort,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
srPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads
start,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
startIndex MIndex objects
startIndex,ByPos_MIndex-method MIndex objects
stringDist String Distance/Alignment Score Matrix
stringDist,character-method String Distance/Alignment Score Matrix
stringDist,QualityScaledXStringSet-method String Distance/Alignment Score Matrix
stringDist,XStringSet-method String Distance/Alignment Score Matrix
strrev Function to calculate the frequency of letters in a biological sequence and related functions
subBString Fast substring extraction
subject,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
subpatterns XStringPartialMatches objects
subpatterns,XStringPartialMatches-method XStringPartialMatches objects
subseq,MaskedXString-method MaskedXString objects
substitution.matrices Scoring matrices
substr Fast substring extraction
substr,MaskedXString-method Fast substring extraction
substr,XString-method Fast substring extraction
substring Fast substring extraction
substring,MaskedXString-method Fast substring extraction
substring,XString-method Fast substring extraction
subXString Fast substring extraction
summary,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects

-- T --

tail,PDict3Parts-method PDict objects
tail,TB_PDict-method PDict objects
tb PDict objects
tb,PDict3Parts-method PDict objects
tb,PreprocessedTB-method PDict objects
tb,TB_PDict-method PDict objects
tb.width PDict objects
tb.width,PDict3Parts-method PDict objects
tb.width,PreprocessedTB-method PDict objects
tb.width,TB_PDict-method PDict objects
TB_PDict PDict objects
TB_PDict-class PDict objects
toComplex Turning a DNA sequence into a vector of complex numbers
toComplex,DNAString-method Turning a DNA sequence into a vector of complex numbers
toString,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
toString,MaskedXString-method MaskedXString objects
toString,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
toString,XString-method BString objects
toString,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
toString,XStringViews-method The XStringViews class
transcribe DNA/RNA transcription and translation
translate DNA/RNA transcription and translation
translate,DNAString-method DNA/RNA transcription and translation
translate,DNAStringSet-method DNA/RNA transcription and translation
translate,MaskedDNAString-method DNA/RNA transcription and translation
translate,MaskedRNAString-method DNA/RNA transcription and translation
translate,RNAString-method DNA/RNA transcription and translation
translate,RNAStringSet-method DNA/RNA transcription and translation
trinucleotideFrequency Function to calculate the frequency of letters in a biological sequence and related functions
Twobit PDict objects
Twobit-class PDict objects
type PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
type,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
type,PairwiseAlignedFixedSubjectSummary-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects

-- U --

unaligned AlignedXStringSet and QualityAlignedXStringSet objects
unaligned,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
uniqueLetters Function to calculate the frequency of letters in a biological sequence and related functions
uniqueLetters,MaskedXString-method Function to calculate the frequency of letters in a biological sequence and related functions
uniqueLetters,XString-method Function to calculate the frequency of letters in a biological sequence and related functions
uniqueLetters,XStringSet-method Function to calculate the frequency of letters in a biological sequence and related functions
uniqueLetters,XStringViews-method Function to calculate the frequency of letters in a biological sequence and related functions
unlist,MIndex-method MIndex objects
unmasked MaskedXString objects
unmasked,MaskedXString-method MaskedXString objects

-- V --

vcountPattern String searching functions
vcountPattern,character-method String searching functions
vcountPattern,MaskedXString-method String searching functions
vcountPattern,XString-method String searching functions
vcountPattern,XStringSet-method String searching functions
vcountPattern,XStringViews-method String searching functions
vcountPDict Searching a sequence for patterns stored in a preprocessed dictionary
vcountPDict,MaskedXString-method Searching a sequence for patterns stored in a preprocessed dictionary
vcountPDict,XString-method Searching a sequence for patterns stored in a preprocessed dictionary
vcountPDict,XStringSet-method Searching a sequence for patterns stored in a preprocessed dictionary
vcountPDict,XStringViews-method Searching a sequence for patterns stored in a preprocessed dictionary
Views,character-method The XStringViews class
Views,MaskedXString-method MaskedXString objects
Views,PairwiseAlignedFixedSubject-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
Views,XString-method The XStringViews class
vmatchPattern String searching functions
vmatchPattern,character-method String searching functions
vmatchPattern,MaskedXString-method String searching functions
vmatchPattern,XString-method String searching functions
vmatchPattern,XStringSet-method String searching functions
vmatchPattern,XStringViews-method String searching functions
vmatchPDict Searching a sequence for patterns stored in a preprocessed dictionary
vmatchPDict,ANY-method Searching a sequence for patterns stored in a preprocessed dictionary
vmatchPDict,MaskedXString-method Searching a sequence for patterns stored in a preprocessed dictionary
vmatchPDict,XString-method Searching a sequence for patterns stored in a preprocessed dictionary

-- W --

whichPDict Searching a sequence for patterns stored in a preprocessed dictionary
whichPDict,XString-method Searching a sequence for patterns stored in a preprocessed dictionary
width,AlignedXStringSet-method AlignedXStringSet and QualityAlignedXStringSet objects
width,PDict-method PDict objects
width,PDict3Parts-method PDict objects
width,PreprocessedTB-method PDict objects
width,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
write.BStringViews Read/write an XStringSet or XStringViews object from/to a file
write.XStringSet Read/write an XStringSet or XStringViews object from/to a file
write.XStringViews Read/write an XStringSet or XStringViews object from/to a file
writeFASTA Functions to read/write FASTA formatted files
wtPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads

-- X --

XString BString objects
XString,AsIs-method BString objects
XString,character-method BString objects
XString,MaskedXString-method MaskedXString objects
XString,XString-method BString objects
XString-class BString objects
XStringPartialMatches-class XStringPartialMatches objects
XStringQuality PhredQuality and SolexaQuality objects
XStringQuality-class PhredQuality and SolexaQuality objects
XStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,AsIs-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,character-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XString-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet,XStringViews-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringSetToFASTArecords Read/write an XStringSet or XStringViews object from/to a file
XStringViews Basic functions for creating or modifying XStringViews objects
XStringViews,ANY-method Basic functions for creating or modifying XStringViews objects
XStringViews,XString-method Basic functions for creating or modifying XStringViews objects
XStringViews,XStringViews-method Basic functions for creating or modifying XStringViews objects
XStringViews-class The XStringViews class
XStringViews-constructors Basic functions for creating or modifying XStringViews objects

-- Y --

yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package

-- misc --

[,ACtree,ANY,ANY,ANY-method PDict objects
[,AlignedXStringSet,ANY,ANY,ANY-method AlignedXStringSet and QualityAlignedXStringSet objects
[,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
[,QualityAlignedXStringSet,ANY,ANY,ANY-method AlignedXStringSet and QualityAlignedXStringSet objects
[,QualityScaledXStringSet,ANY,ANY,ANY-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
[,XString,ANY,ANY,ANY-method BString objects
[,XStringPartialMatches,ANY,ANY,ANY-method XStringPartialMatches objects
[,XStringSet,ANY,ANY,ANY-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[<-,AlignedXStringSet,ANY,ANY,ANY-method AlignedXStringSet and QualityAlignedXStringSet objects
[<-,PairwiseAlignedFixedSubject,ANY,ANY,ANY-method PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects
[[,ByPos_MIndex-method MIndex objects
[[,PDict-method PDict objects
[[,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[<-,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects