String objects representing biological sequences, and matching algorithms


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Documentation for package ‘Biostrings’ version 2.8.18

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A B C D E F G H I L M N O P 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
$,MIndex-method Searching a sequence for patterns stored in a dictionary
.inplaceReplaceLetterAtLoc 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
AAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,ANY-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,character-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,vector-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringList-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
AA_ALPHABET AAString objects
active MaskCollection objects
active,MaskCollection-method MaskCollection objects
active<-,MaskCollection-method MaskCollection objects
ACtree PDict objects
ACtree-class PDict objects
adjacentViews Basic functions for creating or modifying XStringViews objects
align1 XStringAlign objects
align1,XStringAlign-method XStringAlign objects
align2 XStringAlign objects
align2,XStringAlign-method XStringAlign objects
alignScore (Deprecated) Needleman-Wunsch Global Alignment
alphabet BString objects
alphabet,AAString-method AAString objects
alphabet,BString-method BString objects
alphabet,DNAString-method DNAString objects
alphabet,MaskedXString-method MaskedXString objects
alphabet,RNAString-method RNAString objects
alphabet,XStringAlign-method XStringAlign objects
alphabet,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
alphabet,XStringViews-method The XStringViews class
alphabetFrequency Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAString-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,DNAStringSet-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,MaskedXString-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAString-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,RNAStringSet-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XString-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XStringSet-method Functions to calculate the frequency of letters in a biological sequence
alphabetFrequency,XStringViews-method Functions to calculate the frequency of letters in a biological sequence
AMINO_ACID_CODE The Single-Letter Amino Acid Code
append,MaskCollection-method MaskCollection objects
as.character,MaskedXString-method MaskedXString objects
as.character,XString-method BString objects
as.character,XStringAlign-method XStringAlign objects
as.character,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.character,XStringViews-method The XStringViews class
as.complex,DNAString-method Converting a DNAString to a vector of complexes
as.data.frame,IRanges-method IRanges and NormalIRanges objects
as.list,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.list,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
as.list,XStringViews-method The XStringViews class
as.matrix,ACtree-method PDict objects
as.matrix,IRanges-method IRanges and NormalIRanges objects
as.matrix,XStringViews-method The XStringViews class

-- 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
BStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,ANY-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,character-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,vector-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
BStringList-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet 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
ByName_MIndex-class Searching a sequence for patterns stored in a dictionary
ByPos_MIndex-class Searching a sequence for patterns stored in a dictionary

-- C --

cDNA Sequence reversing and complementing
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:AAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:AAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ACtree PDict objects
class:BOC2_SubjectString BOC_SubjectString and BOC2_SubjectString objects
class:BOC_SubjectString BOC_SubjectString and BOC2_SubjectString objects
class:BString BString objects
class:BStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:BStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:ByName_MIndex Searching a sequence for patterns stored in a dictionary
class:ByPos_MIndex Searching a sequence for patterns stored in a dictionary
class:CWdna_PDict PDict objects
class:DNAString DNAString objects
class:DNAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:DNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:Dups PDict objects
class:IRanges IRanges and NormalIRanges objects
class:LockedIRanges IRanges and NormalIRanges objects
class:MaskCollection MaskCollection objects
class:MaskedAAString MaskedXString objects
class:MaskedBString MaskedXString objects
class:MaskedDNAString MaskedXString objects
class:MaskedRNAString MaskedXString objects
class:MaskedXString MaskedXString objects
class:MIndex Searching a sequence for patterns stored in a dictionary
class:NormalIRanges IRanges and NormalIRanges objects
class:PDict PDict objects
class:RNAString RNAString objects
class:RNAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:RNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:TBdna_PDict PDict objects
class:UnlockedIRanges IRanges and NormalIRanges objects
class:Views IRanges and NormalIRanges objects
class:XString BString objects
class:XStringAlign XStringAlign objects
class:XStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:XStringPartialMatches XStringPartialMatches objects
class:XStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
class:XStringViews The XStringViews class
coerce,AAString,MaskedAAString-method MaskedXString objects
coerce,BString,MaskedBString-method MaskedXString objects
coerce,DNAString,MaskedDNAString-method MaskedXString objects
coerce,IRanges,NormalIRanges-method IRanges and NormalIRanges objects
coerce,LockedIRanges,NormalIRanges-method IRanges and NormalIRanges objects
coerce,MaskCollection,NormalIRanges-method MaskCollection 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,RNAString,MaskedRNAString-method MaskedXString objects
coerce,UnlockedIRanges,NormalIRanges-method IRanges and NormalIRanges objects
coerce,Views,NormalIRanges-method IRanges and NormalIRanges objects
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
consmat Utility functions related to sequence alignment
consmat,character-method Utility functions related to sequence alignment
consmat,list-method Utility functions related to sequence alignment
consmat,matrix-method Utility functions related to sequence alignment
consmat,XStringAlign-method Utility functions related to sequence alignment
consmat,XStringSet-method Utility functions related to sequence alignment
consmat,XStringViews-method Utility functions related to sequence alignment
countIndex Searching a sequence for patterns stored in a dictionary
countIndex,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
countIndex,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
countIndex,MIndex-method Searching a sequence for patterns stored in a dictionary
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,XStringViews-method String searching functions
countPDict Searching a sequence for patterns stored in a dictionary
countPDict,MaskedXString-method Searching a sequence for patterns stored in a dictionary
countPDict,XString-method Searching a sequence for patterns stored in a dictionary
countPDict,XStringViews-method Searching a sequence for patterns stored in a dictionary
countPWM A simple PWM matching function and related utilities
coverage Utility functions related to pattern matching
coverage,IRanges-method Utility functions related to pattern matching
coverage,MaskCollection-method Utility functions related to pattern matching
coverage,MaskedXString-method Utility functions related to pattern matching
coverage,MIndex-method Utility functions related to pattern matching
coverage,XStringViews-method Utility functions related to pattern matching
CWdna_PDict PDict objects
CWdna_PDict-class PDict objects

-- D --

desc IRanges and NormalIRanges objects
dinucleotideFrequency Functions to calculate the frequency of letters in a biological sequence
dna2rna Sequence reversing and complementing
DNAString DNAString objects
DNAString-class DNAString objects
DNAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,ANY-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,character-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,vector-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringList-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
DNA_ALPHABET DNAString objects
duplicated,CWdna_PDict-method PDict objects
duplicated,Dups-method PDict objects
duplicated,IRanges-method IRanges and NormalIRanges objects
duplicated,TBdna_PDict-method PDict objects
Dups PDict objects
Dups-class PDict objects

-- E --

end,IRanges-method IRanges and NormalIRanges objects
end<-,UnlockedIRanges-method IRanges and NormalIRanges objects
endIndex Searching a sequence for patterns stored in a dictionary
endIndex,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
endIndex,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
extractAllMatches Searching a sequence for patterns stored in a dictionary

-- F --

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
first IRanges and NormalIRanges objects
first,IRanges-method IRanges and NormalIRanges objects

-- G --

gaps IRanges utility functions
gaps,IRanges-method IRanges utility functions
gaps,MaskCollection-method MaskCollection objects
gaps,MaskedXString-method MaskedXString objects
gaps,XStringViews-method Basic functions for creating or modifying XStringViews objects
GENETIC_CODE The Standard Genetic Code
gregexpr2 A replacement for R standard gregexpr function

-- H --

head,TBdna_PDict-method PDict objects

-- I --

initialize,AAStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,ACtree-method PDict objects
initialize,BOC2_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
initialize,BOC_SubjectString-method BOC_SubjectString and BOC2_SubjectString objects
initialize,BStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,CWdna_PDict-method PDict objects
initialize,DNAStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,IRanges-method IRanges and NormalIRanges objects
initialize,NormalIRanges-method IRanges and NormalIRanges objects
initialize,RNAStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,TBdna_PDict-method PDict objects
initialize,Views-method IRanges and NormalIRanges objects
initialize,XStringAlign-method XStringAlign objects
initialize,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
initialize,XStringViews-method The XStringViews class
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
intToAdjacentRanges IRanges utility functions
intToRanges IRanges utility functions
IRanges IRanges and NormalIRanges objects
IRanges-class IRanges and NormalIRanges objects
IRanges-utils IRanges utility functions
isEmpty IRanges and NormalIRanges objects
isEmpty,IRanges-method IRanges and NormalIRanges objects
isEmpty,MaskCollection-method MaskCollection objects
isEmpty,NormalIRanges-method IRanges and NormalIRanges objects
isMatching Utility functions related to pattern matching
isMatching,character-method Utility functions related to pattern matching
isMatching,XString-method Utility functions related to pattern matching
isNormal IRanges and NormalIRanges objects
isNormal,IRanges-method IRanges and NormalIRanges objects
IUPAC_CODE_MAP The IUPAC Extended Genetic Alphabet

-- L --

last IRanges and NormalIRanges objects
last,IRanges-method IRanges and NormalIRanges objects
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,ACtree-method PDict objects
length,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
length,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
length,CWdna_PDict-method PDict objects
length,Dups-method PDict objects
length,IRanges-method IRanges and NormalIRanges objects
length,MaskCollection-method MaskCollection objects
length,MaskedXString-method MaskedXString objects
length,XString-method BString objects
length,XStringAlign-method XStringAlign objects
length,XStringList-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
LockedIRanges IRanges and NormalIRanges objects
LockedIRanges-class IRanges and NormalIRanges objects

-- M --

Mask MaskCollection objects
mask Masking by content (or by position)
MaskCollection MaskCollection objects
MaskCollection-class MaskCollection objects
MaskedAAString MaskedXString objects
MaskedAAString-class MaskedXString objects
MaskedBString MaskedXString objects
MaskedBString-class MaskedXString objects
MaskedDNAString MaskedXString objects
MaskedDNAString-class MaskedXString objects
maskedratio MaskCollection objects
maskedratio,MaskCollection-method MaskCollection objects
maskedratio,MaskedXString-method MaskedXString objects
MaskedRNAString MaskedXString objects
MaskedRNAString-class MaskedXString objects
maskedwidth MaskCollection objects
maskedwidth,MaskCollection-method MaskCollection 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 patterns defined by a left and a right part in a sequence
matchLRPatterns,MaskedXString-method Find patterns defined by a left and a right part in a sequence
matchLRPatterns,XString-method Find patterns defined by a left and a right part in a sequence
matchLRPatterns,XStringViews-method Find patterns defined by a left and a right part 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,XStringViews-method String searching functions
matchPDict Searching a sequence for patterns stored in a dictionary
matchPDict,MaskedXString-method Searching a sequence for patterns stored in a dictionary
matchPDict,XString-method Searching a sequence for patterns stored in a dictionary
matchPDict,XStringViews-method Searching a sequence for patterns stored in a dictionary
matchPDict-exact Searching a sequence for patterns stored in a dictionary
matchPDict-inexact Inexact matching with matchPDict()
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
max,MaskCollection-method MaskCollection objects
max,NormalIRanges-method IRanges and NormalIRanges objects
maxScore A simple PWM matching function and related utilities
maxWeights A simple PWM matching function and related utilities
mergeIUPACLetters The IUPAC Extended Genetic Alphabet
min,MaskCollection-method MaskCollection objects
min,NormalIRanges-method IRanges and NormalIRanges objects
MIndex Searching a sequence for patterns stored in a dictionary
MIndex-class Searching a sequence for patterns stored in a dictionary
mismatch Utility functions related to pattern matching
mismatch,XStringViews-method Utility functions related to pattern matching
mkAllStrings Functions to calculate the frequency of letters in a biological sequence

-- N --

names,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
names,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
names,CWdna_PDict-method PDict objects
names,IRanges-method IRanges and NormalIRanges objects
names,MaskCollection-method MaskCollection objects
names,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
names<-,IRanges-method IRanges and NormalIRanges objects
names<-,MaskCollection-method MaskCollection objects
names<-,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
narrow IRanges utility functions
narrow,IRanges-method IRanges utility functions
narrow,MaskCollection-method MaskCollection objects
narrow,NormalIRanges-method IRanges utility functions
narrow,numeric-method IRanges utility functions
narrow,XStringViews-method Basic functions for creating or modifying XStringViews objects
nchar,MaskedXString-method MaskedXString objects
nchar,XString-method BString objects
nchar,XStringAlign-method XStringAlign objects
nchar,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
nchar,XStringViews-method The XStringViews class
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
nir_list MaskCollection objects
nir_list,MaskCollection-method MaskCollection objects
nmismatchEndingAt Utility functions related to pattern matching
nmismatchEndingAt,character-method Utility functions related to pattern matching
nmismatchEndingAt,XString-method Utility functions related to pattern matching
nmismatchStartingAt Utility functions related to pattern matching
nmismatchStartingAt,character-method Utility functions related to pattern matching
nmismatchStartingAt,XString-method Utility functions related to pattern matching
NormalIRanges IRanges and NormalIRanges objects
NormalIRanges-class IRanges and NormalIRanges objects

-- O --

oligonucleotideFrequency Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,DNAString-method Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,MaskedXString-method Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,RNAString-method Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,XStringSet-method Functions to calculate the frequency of letters in a biological sequence
oligonucleotideFrequency,XStringViews-method Functions to calculate the frequency of letters in a biological sequence

-- P --

pairwiseAlignment Optimal Pairwise Alignment
pairwiseAlignment,character,character-method Optimal Pairwise Alignment
pairwiseAlignment,character,XString-method Optimal Pairwise Alignment
pairwiseAlignment,XString,character-method Optimal Pairwise Alignment
pairwiseAlignment,XString,XString-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,XStringPartialMatches-method XStringPartialMatches objects
patternFrequency PDict objects
patternFrequency,CWdna_PDict-method PDict objects
patternFrequency,TBdna_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
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
print.needwunsQS (Deprecated) Needleman-Wunsch Global Alignment
PWMscore A simple PWM matching function and related utilities

-- R --

read.AAStringSet Read/write an XStringSet or XStringViews object from/to a file
read.agpMask Read a mask from 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.gapMask Read a mask from a file
read.liftMask Read a mask from a file
read.Mask Read a mask from a file
read.rmMask Read a mask from a file
read.RNAStringSet Read/write an XStringSet or XStringViews object from/to a file
read.trfMask Read a mask from a file
read.XStringViews Read/write an XStringSet or XStringViews object from/to a file
readFASTA Functions to read/write FASTA formatted files
reduce IRanges utility functions
reduce,IRanges-method IRanges utility functions
reduce,MaskCollection-method MaskCollection objects
reduce,MaskedXString-method MaskedXString objects
replaceLetterAtLoc Replacing letters in a sequence at some specified locations
replaceLetterAtLoc,DNAString-method Replacing letters in a sequence at some specified locations
restrict IRanges utility functions
restrict,IRanges-method IRanges utility functions
restrict,XStringViews-method Basic functions for creating or modifying XStringViews objects
reverse Sequence reversing and complementing
reverse,IRanges-method Sequence reversing and complementing
reverse,MaskCollection-method Sequence reversing and complementing
reverse,MaskedXString-method Sequence reversing and complementing
reverse,NormalIRanges-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 Sequence reversing and complementing
RNAString RNAString objects
RNAString-class RNAString objects
RNAStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,ANY-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,character-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,vector-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringList-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringSet BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNAStringSet-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
RNA_ALPHABET RNAString objects

-- S --

score XStringAlign objects
score,XStringAlign-method XStringAlign objects
shift IRanges utility functions
shift,IRanges-method IRanges utility functions
show,ACtree-method PDict objects
show,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
show,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
show,CWdna_PDict-method PDict objects
show,IRanges-method IRanges and NormalIRanges objects
show,MaskCollection-method MaskCollection objects
show,MaskedXString-method MaskedXString objects
show,TBdna_PDict-method PDict objects
show,XString-method BString objects
show,XStringAlign-method XStringAlign objects
show,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
show,XStringPartialMatches-method XStringPartialMatches objects
show,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
show,XStringViews-method The XStringViews class
start,IRanges-method IRanges and NormalIRanges objects
start<-,UnlockedIRanges-method IRanges and NormalIRanges objects
startIndex Searching a sequence for patterns stored in a dictionary
startIndex,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
startIndex,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
startIndex,MIndex-method Searching a sequence for patterns stored in a dictionary
strrev Functions to calculate the frequency of letters in a biological sequence
subBString Fast substring extraction
subject The XStringViews class
subject,XStringViews-method The XStringViews class
subpatterns XStringPartialMatches objects
subpatterns,XStringPartialMatches-method XStringPartialMatches objects
subseq BString objects
subseq,MaskedXString-method MaskedXString objects
subseq,XString-method BString objects
substitution.matrices Scoring matrices
substr Fast substring extraction
substr,XString-method Fast substring extraction
substring Fast substring extraction
substring,XString-method Fast substring extraction
subviews Basic functions for creating or modifying XStringViews objects
subXString Fast substring extraction

-- T --

tail,TBdna_PDict-method PDict objects
TBdna_PDict PDict objects
TBdna_PDict-class PDict objects
toComplex Converting a DNAString to a vector of complexes
toComplex,DNAString-method Converting a DNAString to a vector of complexes
toNormalIRanges IRanges utility functions
toString,MaskedXString-method MaskedXString objects
toString,XString-method BString objects
toString,XStringViews-method The XStringViews class
transcribe Sequence reversing and complementing
trim Basic functions for creating or modifying XStringViews objects
trinucleotideFrequency Functions to calculate the frequency of letters in a biological sequence
type XStringAlign objects
type,XStringAlign-method XStringAlign objects

-- U --

unlist Searching a sequence for patterns stored in a dictionary
unlist,MIndex-method Searching a sequence for patterns stored in a dictionary
UnlockedIRanges IRanges and NormalIRanges objects
UnlockedIRanges-class IRanges and NormalIRanges objects
unmasked MaskedXString objects
unmasked,MaskedXString-method MaskedXString objects
update,UnlockedIRanges-method IRanges and NormalIRanges objects

-- V --

vcountPattern String searching functions
vcountPattern,character-method String searching functions
vcountPattern,XStringSet-method String searching functions
Views IRanges and NormalIRanges objects
views Basic functions for creating or modifying XStringViews objects
Views-class IRanges and NormalIRanges objects

-- W --

whichFirstNotNormal IRanges and NormalIRanges objects
whichFirstNotNormal,IRanges-method IRanges and NormalIRanges objects
width IRanges and NormalIRanges objects
width,CWdna_PDict-method PDict objects
width,IRanges-method IRanges and NormalIRanges objects
width,MaskCollection-method MaskCollection objects
width,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
width<-,UnlockedIRanges-method IRanges and NormalIRanges objects
width<-,XStringViews-method The XStringViews class
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

-- 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
XStringAlign XStringAlign objects
XStringAlign-class XStringAlign objects
XStringList BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringList-class BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
XStringPartialMatches-class XStringPartialMatches 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,file-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-method PDict objects
[,IRanges-method IRanges and NormalIRanges objects
[,MaskCollection-method MaskCollection objects
[,XString-method BString objects
[,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[,XStringPartialMatches-method XStringPartialMatches objects
[<-,IRanges-method IRanges and NormalIRanges objects
[<-,MaskCollection-method MaskCollection objects
[<-,XString-method BString objects
[<-,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,ByName_MIndex-method Searching a sequence for patterns stored in a dictionary
[[,ByPos_MIndex-method Searching a sequence for patterns stored in a dictionary
[[,MaskCollection-method MaskCollection objects
[[,MIndex-method Searching a sequence for patterns stored in a dictionary
[[,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[,XStringViews-method The XStringViews class
[[<-,MaskCollection-method MaskCollection objects
[[<-,XStringList-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[<-,XStringSet-method BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
[[<-,XStringViews-method The XStringViews class