!=,BString,character-method	XString-class
!=,character,BString-method	XString-class
!=,character,XStringViews-method	XStringViews-class
!=,XInteger,XInteger-method	Biostrings-internals
!=,XRaw,XRaw-method	Biostrings-internals
!=,XString,XString-method	XString-class
!=,XString,XStringViews-method	XStringViews-class
!=,XStringViews,character-method	XStringViews-class
!=,XStringViews,XString-method	XStringViews-class
!=,XStringViews,XStringViews-method	XStringViews-class
$,MIndex-method	matchPDict-exact
.inplaceReplaceLetterAtLoc	replaceLetterAtLoc
==,BString,character-method	XString-class
==,character,BString-method	XString-class
==,character,XStringViews-method	XStringViews-class
==,XInteger,XInteger-method	Biostrings-internals
==,XRaw,XRaw-method	Biostrings-internals
==,XString,XString-method	XString-class
==,XString,XStringViews-method	XStringViews-class
==,XStringViews,character-method	XStringViews-class
==,XStringViews,XString-method	XStringViews-class
==,XStringViews,XStringViews-method	XStringViews-class
AAString	AAString-class
AAString-class	AAString-class
AAStringList	XStringSet-class
AAStringList,ANY-method	XStringSet-class
AAStringList,character-method	XStringSet-class
AAStringList,vector-method	XStringSet-class
AAStringList,XStringList-method	XStringSet-class
AAStringList-class	XStringSet-class
AAStringSet	XStringSet-class
AAStringSet-class	XStringSet-class
AA_ALPHABET	AAString-class
active	MaskCollection-class
active,MaskCollection-method	MaskCollection-class
active<-	MaskCollection-class
active<-,MaskCollection-method	MaskCollection-class
ACtree	PDict-class
ACtree-class	PDict-class
adjacentViews	XStringViews-constructors
align1	XStringAlign-class
align1,XStringAlign-method	XStringAlign-class
align2	XStringAlign-class
align2,XStringAlign-method	XStringAlign-class
alignScore	needwunsQS
alignScore.needwunsQS	needwunsQS
alphabet	XString-class
alphabet,AAString-method	AAString-class
alphabet,BString-method	XString-class
alphabet,DNAString-method	DNAString-class
alphabet,MaskedXString-method	MaskedXString-class
alphabet,RNAString-method	RNAString-class
alphabet,XStringAlign-method	XStringAlign-class
alphabet,XStringCodec-method	Biostrings-internals
alphabet,XStringSet-method	XStringSet-class
alphabet,XStringViews-method	XStringViews-class
alphabetFrequency	alphabetFrequency
alphabetFrequency,DNAString-method	alphabetFrequency
alphabetFrequency,DNAStringSet-method	alphabetFrequency
alphabetFrequency,MaskedXString-method	alphabetFrequency
alphabetFrequency,RNAString-method	alphabetFrequency
alphabetFrequency,RNAStringSet-method	alphabetFrequency
alphabetFrequency,XString-method	alphabetFrequency
alphabetFrequency,XStringSet-method	alphabetFrequency
alphabetFrequency,XStringViews-method	alphabetFrequency
AMINO_ACID_CODE	AMINO_ACID_CODE
append,MaskCollection-method	MaskCollection-class
as.character,MaskedXString-method	MaskedXString-class
as.character,XString-method	XString-class
as.character,XStringAlign-method	XStringAlign-class
as.character,XStringSet-method	XStringSet-class
as.character,XStringViews-method	XStringViews-class
as.complex,DNAString-method	toComplex
as.data.frame,IRanges-method	IRanges-class
as.integer,XInteger-method	Biostrings-internals
as.integer,XRaw-method	Biostrings-internals
as.list,SparseList-method	Biostrings-internals
as.list,XStringList-method	XStringSet-class
as.list,XStringSet-method	XStringSet-class
as.list,XStringViews-method	XStringViews-class
as.matrix,ACtree-method	PDict-class
as.matrix,IRanges-method	IRanges-class
as.matrix,XStringViews-method	XStringViews-class
BLOSUM100	substitution_matrices
BLOSUM45	substitution_matrices
BLOSUM50	substitution_matrices
BLOSUM62	substitution_matrices
BLOSUM80	substitution_matrices
BOC2_SubjectString	BOC_SubjectString-class
BOC2_SubjectString-class	BOC_SubjectString-class
BOC_SubjectString	BOC_SubjectString-class
BOC_SubjectString-class	BOC_SubjectString-class
BString	XString-class
BString-class	XString-class
BStringList	XStringSet-class
BStringList,ANY-method	XStringSet-class
BStringList,character-method	XStringSet-class
BStringList,vector-method	XStringSet-class
BStringList,XStringList-method	XStringSet-class
BStringList-class	XStringSet-class
BStringSet	XStringSet-class
BStringSet-class	XStringSet-class
BStringViews	XStringViews-constructors
BStringViews,ANY-method	XStringViews-constructors
BStringViews,file-method	XStringViews-constructors
BStringViews,XString-method	XStringViews-constructors
BStringViews,XStringViews-method	XStringViews-constructors
ByName_MIndex-class	matchPDict-exact
ByPos_MIndex-class	matchPDict-exact
cDNA	reverse
CharacterToFASTArecords	XStringSet-io
chartr	chartr
chartr,MaskedXString-method	chartr
chartr,XString-method	chartr
chartr,XStringSet-method	chartr
chartr,XStringViews-method	chartr
class:AAString	AAString-class
class:AAStringList	XStringSet-class
class:AAStringSet	XStringSet-class
class:ACtree	PDict-class
class:BOC2_SubjectString	BOC_SubjectString-class
class:BOC_SubjectString	BOC_SubjectString-class
class:BString	XString-class
class:BStringList	XStringSet-class
class:BStringSet	XStringSet-class
class:ByName_MIndex	matchPDict-exact
class:ByPos_MIndex	matchPDict-exact
class:CWdna_PDict	PDict-class
class:DNAString	DNAString-class
class:DNAStringList	XStringSet-class
class:DNAStringSet	XStringSet-class
class:Dups	PDict-class
class:IRanges	IRanges-class
class:LockedIRanges	IRanges-class
class:MaskCollection	MaskCollection-class
class:MaskedAAString	MaskedXString-class
class:MaskedBString	MaskedXString-class
class:MaskedDNAString	MaskedXString-class
class:MaskedRNAString	MaskedXString-class
class:MaskedXString	MaskedXString-class
class:MIndex	matchPDict-exact
class:NormalIRanges	IRanges-class
class:PDict	PDict-class
class:PrintableXRaw	Biostrings-internals
class:RNAString	RNAString-class
class:RNAStringList	XStringSet-class
class:RNAStringSet	XStringSet-class
class:SparseList	Biostrings-internals
class:TBdna_PDict	PDict-class
class:UnlockedIRanges	IRanges-class
class:Views	IRanges-class
class:XInteger	Biostrings-internals
class:XRaw	Biostrings-internals
class:XString	XString-class
class:XStringAlign	XStringAlign-class
class:XStringCodec	Biostrings-internals
class:XStringList	XStringSet-class
class:XStringPartialMatches	XStringPartialMatches-class
class:XStringSet	XStringSet-class
class:XStringViews	XStringViews-class
coerce,AAString,MaskedAAString-method	MaskedXString-class
coerce,BString,MaskedBString-method	MaskedXString-class
coerce,DNAString,MaskedDNAString-method	MaskedXString-class
coerce,IRanges,NormalIRanges-method	IRanges-class
coerce,LockedIRanges,NormalIRanges-method	IRanges-class
coerce,MaskCollection,NormalIRanges-method	MaskCollection-class
coerce,MaskedAAString,AAString-method	MaskedXString-class
coerce,MaskedBString,BString-method	MaskedXString-class
coerce,MaskedDNAString,DNAString-method	MaskedXString-class
coerce,MaskedRNAString,RNAString-method	MaskedXString-class
coerce,MaskedXString,MaskCollection-method	MaskedXString-class
coerce,MaskedXString,NormalIRanges-method	MaskedXString-class
coerce,MaskedXString,XStringViews-method	MaskedXString-class
coerce,RNAString,MaskedRNAString-method	MaskedXString-class
coerce,UnlockedIRanges,NormalIRanges-method	IRanges-class
coerce,Views,NormalIRanges-method	IRanges-class
complement	reverse
complement,DNAString-method	reverse
complement,DNAStringSet-method	reverse
complement,MaskedDNAString-method	reverse
complement,MaskedRNAString-method	reverse
complement,RNAString-method	reverse
complement,RNAStringSet-method	reverse
complement,XStringViews-method	reverse
complementedPalindromeArmLength	findPalindromes
complementedPalindromeArmLength,DNAString-method	findPalindromes
complementedPalindromeArmLength,XStringViews-method	findPalindromes
complementedPalindromeLeftArm	findPalindromes
complementedPalindromeLeftArm,DNAString-method	findPalindromes
complementedPalindromeLeftArm,XStringViews-method	findPalindromes
complementedPalindromeRightArm	findPalindromes
complementedPalindromeRightArm,DNAString-method	findPalindromes
complementedPalindromeRightArm,XStringViews-method	findPalindromes
consmat	align-utils
consmat,character-method	align-utils
consmat,list-method	align-utils
consmat,matrix-method	align-utils
consmat,XStringAlign-method	align-utils
consmat,XStringSet-method	align-utils
consmat,XStringViews-method	align-utils
countIndex	matchPDict-exact
countIndex,ByName_MIndex-method	matchPDict-exact
countIndex,ByPos_MIndex-method	matchPDict-exact
countIndex,MIndex-method	matchPDict-exact
countPattern	matchPattern
countPattern,BOC2_SubjectString-method	BOC_SubjectString-class
countPattern,character-method	matchPattern
countPattern,MaskedXString-method	matchPattern
countPattern,XString-method	matchPattern
countPattern,XStringViews-method	matchPattern
countPDict	matchPDict-exact
countPDict,MaskedXString-method	matchPDict-exact
countPDict,XString-method	matchPDict-exact
countPDict,XStringViews-method	matchPDict-exact
countPWM	matchPWM
coverage	match-utils
coverage,IRanges-method	match-utils
coverage,MaskCollection-method	match-utils
coverage,MaskedXString-method	match-utils
coverage,MIndex-method	match-utils
coverage,XStringViews-method	match-utils
CWdna_PDict	PDict-class
CWdna_PDict-class	PDict-class
desc	IRanges-class
desc<-	IRanges-class
dinucleotideFrequency	alphabetFrequency
dna2rna	reverse
DNAString	DNAString-class
DNAString-class	DNAString-class
DNAStringList	XStringSet-class
DNAStringList,ANY-method	XStringSet-class
DNAStringList,character-method	XStringSet-class
DNAStringList,vector-method	XStringSet-class
DNAStringList,XStringList-method	XStringSet-class
DNAStringList-class	XStringSet-class
DNAStringSet	XStringSet-class
DNAStringSet-class	XStringSet-class
DNA_ALPHABET	DNAString-class
duplicated,CWdna_PDict-method	PDict-class
duplicated,Dups-method	PDict-class
duplicated,IRanges-method	IRanges-class
duplicated,TBdna_PDict-method	PDict-class
Dups	PDict-class
Dups-class	PDict-class
end,IRanges-method	IRanges-class
end<-	IRanges-class
end<-,UnlockedIRanges-method	IRanges-class
endIndex	matchPDict-exact
endIndex,ByName_MIndex-method	matchPDict-exact
endIndex,ByPos_MIndex-method	matchPDict-exact
extractAllMatches	matchPDict-exact
FASTArecordsToBStringViews	XStringSet-io
FASTArecordsToCharacter	XStringSet-io
FASTArecordsToXStringViews	XStringSet-io
findComplementedPalindromes	findPalindromes
findComplementedPalindromes,DNAString-method	findPalindromes
findComplementedPalindromes,MaskedXString-method	findPalindromes
findComplementedPalindromes,XStringViews-method	findPalindromes
findPalindromes	findPalindromes
findPalindromes,MaskedXString-method	findPalindromes
findPalindromes,XString-method	findPalindromes
findPalindromes,XStringViews-method	findPalindromes
first	IRanges-class
first,IRanges-method	IRanges-class
gaps	IRanges-utils
gaps,IRanges-method	IRanges-utils
gaps,MaskCollection-method	MaskCollection-class
gaps,MaskedXString-method	MaskedXString-class
gaps,XStringViews-method	XStringViews-constructors
GENETIC_CODE	GENETIC_CODE
gregexpr2	gregexpr2
head,TBdna_PDict-method	PDict-class
initialize,AAStringList-method	XStringSet-class
initialize,ACtree-method	PDict-class
initialize,BOC2_SubjectString-method	BOC_SubjectString-class
initialize,BOC_SubjectString-method	BOC_SubjectString-class
initialize,BStringList-method	XStringSet-class
initialize,CWdna_PDict-method	PDict-class
initialize,DNAStringList-method	XStringSet-class
initialize,IRanges-method	IRanges-class
initialize,NormalIRanges-method	IRanges-class
initialize,RNAStringList-method	XStringSet-class
initialize,TBdna_PDict-method	PDict-class
initialize,Views-method	IRanges-class
initialize,XInteger-method	Biostrings-internals
initialize,XRaw-method	Biostrings-internals
initialize,XStringAlign-method	XStringAlign-class
initialize,XStringCodec-method	Biostrings-internals
initialize,XStringSet-method	XStringSet-class
initialize,XStringViews-method	XStringViews-class
injectHardMask	injectHardMask
injectHardMask,MaskedXString-method	injectHardMask
injectHardMask,XStringViews-method	injectHardMask
intToAdjacentRanges	IRanges-utils
intToRanges	IRanges-utils
IRanges	IRanges-class
IRanges-class	IRanges-class
IRanges-utils	IRanges-utils
isEmpty	IRanges-class
isEmpty,IRanges-method	IRanges-class
isEmpty,MaskCollection-method	MaskCollection-class
isEmpty,NormalIRanges-method	IRanges-class
isMatching	match-utils
isMatching,character-method	match-utils
isMatching,XString-method	match-utils
isNormal	IRanges-class
isNormal,IRanges-method	IRanges-class
IUPAC_CODE_MAP	IUPAC_CODE_MAP
last	IRanges-class
last,IRanges-method	IRanges-class
lcprefix	pmatchPattern
lcprefix,character,character-method	pmatchPattern
lcprefix,character,XString-method	pmatchPattern
lcprefix,XString,character-method	pmatchPattern
lcprefix,XString,XString-method	pmatchPattern
lcsubstr	pmatchPattern
lcsubstr,character,character-method	pmatchPattern
lcsubstr,character,XString-method	pmatchPattern
lcsubstr,XString,character-method	pmatchPattern
lcsubstr,XString,XString-method	pmatchPattern
lcsuffix	pmatchPattern
lcsuffix,character,character-method	pmatchPattern
lcsuffix,character,XString-method	pmatchPattern
lcsuffix,XString,character-method	pmatchPattern
lcsuffix,XString,XString-method	pmatchPattern
length,ACtree-method	PDict-class
length,ByName_MIndex-method	matchPDict-exact
length,ByPos_MIndex-method	matchPDict-exact
length,CWdna_PDict-method	PDict-class
length,Dups-method	PDict-class
length,IRanges-method	IRanges-class
length,MaskCollection-method	MaskCollection-class
length,MaskedXString-method	MaskedXString-class
length,SparseList-method	Biostrings-internals
length,XInteger-method	Biostrings-internals
length,XRaw-method	Biostrings-internals
length,XString-method	XString-class
length,XStringAlign-method	XStringAlign-class
length,XStringList-method	XStringSet-class
letter	letter
letter,character-method	letter
letter,MaskedXString-method	letter
letter,XString-method	letter
letter,XStringViews-method	letter
LockedIRanges	IRanges-class
LockedIRanges-class	IRanges-class
ls,SparseList-method	Biostrings-internals
Mask	MaskCollection-class
mask	maskMotif
MaskCollection	MaskCollection-class
MaskCollection-class	MaskCollection-class
MaskedAAString	MaskedXString-class
MaskedAAString-class	MaskedXString-class
MaskedBString	MaskedXString-class
MaskedBString-class	MaskedXString-class
MaskedDNAString	MaskedXString-class
MaskedDNAString-class	MaskedXString-class
maskedratio	MaskCollection-class
maskedratio,MaskCollection-method	MaskCollection-class
maskedratio,MaskedXString-method	MaskedXString-class
MaskedRNAString	MaskedXString-class
MaskedRNAString-class	MaskedXString-class
maskedwidth	MaskCollection-class
maskedwidth,MaskCollection-method	MaskCollection-class
maskedwidth,MaskedXString-method	MaskedXString-class
MaskedXString	MaskedXString-class
MaskedXString-class	MaskedXString-class
maskMotif	maskMotif
maskMotif,MaskedXString,character-method	maskMotif
maskMotif,MaskedXString,XString-method	maskMotif
maskMotif,XString,ANY-method	maskMotif
masks	MaskedXString-class
masks,MaskedXString-method	MaskedXString-class
masks,XString-method	MaskedXString-class
masks<-	MaskedXString-class
masks<-,MaskedXString,MaskCollection-method	MaskedXString-class
masks<-,MaskedXString,NULL-method	MaskedXString-class
masks<-,XString,ANY-method	MaskedXString-class
masks<-,XString,NULL-method	MaskedXString-class
match-utils	match-utils
matchDNAPattern	matchPattern
matchLRPatterns	matchLRPatterns
matchLRPatterns,MaskedXString-method	matchLRPatterns
matchLRPatterns,XString-method	matchLRPatterns
matchLRPatterns,XStringViews-method	matchLRPatterns
matchPattern	matchPattern
matchPattern,BOC2_SubjectString-method	BOC_SubjectString-class
matchPattern,BOC_SubjectString-method	BOC_SubjectString-class
matchPattern,character-method	matchPattern
matchPattern,MaskedXString-method	matchPattern
matchPattern,XString-method	matchPattern
matchPattern,XStringViews-method	matchPattern
matchPDict	matchPDict-exact
matchPDict,MaskedXString-method	matchPDict-exact
matchPDict,XString-method	matchPDict-exact
matchPDict,XStringViews-method	matchPDict-exact
matchPDict-exact	matchPDict-exact
matchPDict-inexact	matchPDict-inexact
matchProbePair	matchProbePair
matchProbePair,DNAString-method	matchProbePair
matchProbePair,MaskedDNAString-method	matchProbePair
matchProbePair,XStringViews-method	matchProbePair
matchPWM	matchPWM
max,MaskCollection-method	MaskCollection-class
max,NormalIRanges-method	IRanges-class
maxScore	matchPWM
maxWeights	matchPWM
mergeIUPACLetters	IUPAC_CODE_MAP
min,MaskCollection-method	MaskCollection-class
min,NormalIRanges-method	IRanges-class
MIndex	matchPDict-exact
MIndex-class	matchPDict-exact
mismatch	match-utils
mismatch,XStringViews-method	match-utils
mkAllStrings	alphabetFrequency
names,ByName_MIndex-method	matchPDict-exact
names,ByPos_MIndex-method	matchPDict-exact
names,CWdna_PDict-method	PDict-class
names,IRanges-method	IRanges-class
names,MaskCollection-method	MaskCollection-class
names,XStringList-method	XStringSet-class
names<-,IRanges-method	IRanges-class
names<-,MaskCollection-method	MaskCollection-class
names<-,XStringList-method	XStringSet-class
narrow	IRanges-utils
narrow,IRanges-method	IRanges-utils
narrow,MaskCollection-method	MaskCollection-class
narrow,NormalIRanges-method	IRanges-utils
narrow,numeric-method	IRanges-utils
narrow,XStringViews-method	XStringViews-constructors
nchar,MaskedXString-method	MaskedXString-class
nchar,XString-method	XString-class
nchar,XStringAlign-method	XStringAlign-class
nchar,XStringList-method	XStringSet-class
nchar,XStringSet-method	XStringSet-class
nchar,XStringViews-method	XStringViews-class
needwunsQS	needwunsQS
needwunsQS,character,character-method	needwunsQS
needwunsQS,character,XString-method	needwunsQS
needwunsQS,XString,character-method	needwunsQS
needwunsQS,XString,XString-method	needwunsQS
nir_list	MaskCollection-class
nir_list,MaskCollection-method	MaskCollection-class
nmismatchEndingAt	match-utils
nmismatchEndingAt,character-method	match-utils
nmismatchEndingAt,XString-method	match-utils
nmismatchStartingAt	match-utils
nmismatchStartingAt,character-method	match-utils
nmismatchStartingAt,XString-method	match-utils
NormalIRanges	IRanges-class
NormalIRanges-class	IRanges-class
oligonucleotideFrequency	alphabetFrequency
oligonucleotideFrequency,DNAString-method	alphabetFrequency
oligonucleotideFrequency,MaskedXString-method	alphabetFrequency
oligonucleotideFrequency,RNAString-method	alphabetFrequency
oligonucleotideFrequency,XStringSet-method	alphabetFrequency
oligonucleotideFrequency,XStringViews-method	alphabetFrequency
pairwiseAlignment	pairwiseAlignment
pairwiseAlignment,character,character-method	pairwiseAlignment
pairwiseAlignment,character,XString-method	pairwiseAlignment
pairwiseAlignment,XString,character-method	pairwiseAlignment
pairwiseAlignment,XString,XString-method	pairwiseAlignment
palindromeArmLength	findPalindromes
palindromeArmLength,XString-method	findPalindromes
palindromeArmLength,XStringViews-method	findPalindromes
palindromeLeftArm	findPalindromes
palindromeLeftArm,XString-method	findPalindromes
palindromeLeftArm,XStringViews-method	findPalindromes
palindromeRightArm	findPalindromes
palindromeRightArm,XString-method	findPalindromes
palindromeRightArm,XStringViews-method	findPalindromes
PAM120	substitution_matrices
PAM250	substitution_matrices
PAM30	substitution_matrices
PAM40	substitution_matrices
PAM70	substitution_matrices
pattern	XStringPartialMatches-class
pattern,XStringPartialMatches-method	XStringPartialMatches-class
patternFrequency	PDict-class
patternFrequency,CWdna_PDict-method	PDict-class
patternFrequency,TBdna_PDict-method	PDict-class
PDict	PDict-class
PDict,AsIs-method	PDict-class
PDict,character-method	PDict-class
PDict,DNAStringSet-method	PDict-class
PDict,XStringViews-method	PDict-class
PDict-class	PDict-class
pmatchPattern	pmatchPattern
pmatchPattern,character-method	pmatchPattern
pmatchPattern,XString-method	pmatchPattern
pmatchPattern,XStringViews-method	pmatchPattern
print.needwunsQS	needwunsQS
PrintableXRaw	Biostrings-internals
PrintableXRaw-class	Biostrings-internals
PWMscore	matchPWM
read.AAStringSet	XStringSet-io
read.agpMask	read.Mask
read.BStringSet	XStringSet-io
read.BStringViews	XStringSet-io
read.DNAStringSet	XStringSet-io
read.gapMask	read.Mask
read.liftMask	read.Mask
read.Mask	read.Mask
read.rmMask	read.Mask
read.RNAStringSet	XStringSet-io
read.trfMask	read.Mask
read.XStringViews	XStringSet-io
readFASTA	readFASTA
reduce	IRanges-utils
reduce,IRanges-method	IRanges-utils
reduce,MaskCollection-method	MaskCollection-class
reduce,MaskedXString-method	MaskedXString-class
replaceLetterAtLoc	replaceLetterAtLoc
replaceLetterAtLoc,DNAString-method	replaceLetterAtLoc
restrict	IRanges-utils
restrict,IRanges-method	IRanges-utils
restrict,XStringViews-method	XStringViews-constructors
reverse	reverse
reverse,IRanges-method	reverse
reverse,MaskCollection-method	reverse
reverse,MaskedXString-method	reverse
reverse,NormalIRanges-method	reverse
reverse,XString-method	reverse
reverse,XStringSet-method	reverse
reverse,XStringViews-method	reverse
reverseComplement	reverse
reverseComplement,DNAString-method	reverse
reverseComplement,DNAStringSet-method	reverse
reverseComplement,MaskedDNAString-method	reverse
reverseComplement,MaskedRNAString-method	reverse
reverseComplement,matrix-method	matchPWM
reverseComplement,RNAString-method	reverse
reverseComplement,RNAStringSet-method	reverse
reverseComplement,XStringViews-method	reverse
rna2dna	reverse
RNAString	RNAString-class
RNAString-class	RNAString-class
RNAStringList	XStringSet-class
RNAStringList,ANY-method	XStringSet-class
RNAStringList,character-method	XStringSet-class
RNAStringList,vector-method	XStringSet-class
RNAStringList,XStringList-method	XStringSet-class
RNAStringList-class	XStringSet-class
RNAStringSet	XStringSet-class
RNAStringSet-class	XStringSet-class
RNA_ALPHABET	RNAString-class
score	XStringAlign-class
score,XStringAlign-method	XStringAlign-class
shift	IRanges-utils
shift,IRanges-method	IRanges-utils
show,ACtree-method	PDict-class
show,ByName_MIndex-method	matchPDict-exact
show,ByPos_MIndex-method	matchPDict-exact
show,CWdna_PDict-method	PDict-class
show,externalptr-method	Biostrings-internals
show,IRanges-method	IRanges-class
show,MaskCollection-method	MaskCollection-class
show,MaskedXString-method	MaskedXString-class
show,PrintableXRaw-method	Biostrings-internals
show,TBdna_PDict-method	PDict-class
show,XInteger-method	Biostrings-internals
show,XRaw-method	Biostrings-internals
show,XString-method	XString-class
show,XStringAlign-method	XStringAlign-class
show,XStringList-method	XStringSet-class
show,XStringPartialMatches-method	XStringPartialMatches-class
show,XStringSet-method	XStringSet-class
show,XStringViews-method	XStringViews-class
SparseList	Biostrings-internals
SparseList-class	Biostrings-internals
start,IRanges-method	IRanges-class
start<-	IRanges-class
start<-,UnlockedIRanges-method	IRanges-class
startIndex	matchPDict-exact
startIndex,ByName_MIndex-method	matchPDict-exact
startIndex,ByPos_MIndex-method	matchPDict-exact
startIndex,MIndex-method	matchPDict-exact
strrev	alphabetFrequency
subBString	subXString
subject	XStringViews-class
subject,XStringViews-method	XStringViews-class
subpatterns	XStringPartialMatches-class
subpatterns,XStringPartialMatches-method	XStringPartialMatches-class
subseq	XString-class
subseq,MaskedXString-method	MaskedXString-class
subseq,XString-method	XString-class
substitution.matrices	substitution_matrices
substr	subXString
substr,XString-method	subXString
substring	subXString
substring,XString-method	subXString
subviews	XStringViews-constructors
subXString	subXString
tail,TBdna_PDict-method	PDict-class
TBdna_PDict	PDict-class
TBdna_PDict-class	PDict-class
toComplex	toComplex
toComplex,DNAString-method	toComplex
toNormalIRanges	IRanges-utils
toString,MaskedXString-method	MaskedXString-class
toString,XRaw-method	Biostrings-internals
toString,XString-method	XString-class
toString,XStringViews-method	XStringViews-class
transcribe	reverse
trim	XStringViews-constructors
trinucleotideFrequency	alphabetFrequency
type	XStringAlign-class
type,XStringAlign-method	XStringAlign-class
unlist	matchPDict-exact
unlist,MIndex-method	matchPDict-exact
UnlockedIRanges	IRanges-class
UnlockedIRanges-class	IRanges-class
unmasked	MaskedXString-class
unmasked,MaskedXString-method	MaskedXString-class
update,UnlockedIRanges-method	IRanges-class
vcountPattern	matchPattern
vcountPattern,character-method	matchPattern
vcountPattern,XStringSet-method	matchPattern
Views	IRanges-class
views	XStringViews-constructors
Views-class	IRanges-class
whichFirstNotNormal	IRanges-class
whichFirstNotNormal,IRanges-method	IRanges-class
width	IRanges-class
width,CWdna_PDict-method	PDict-class
width,IRanges-method	IRanges-class
width,MaskCollection-method	MaskCollection-class
width,XStringList-method	XStringSet-class
width<-	IRanges-class
width<-,UnlockedIRanges-method	IRanges-class
width<-,XStringViews-method	XStringViews-class
write.BStringViews	XStringSet-io
write.XStringSet	XStringSet-io
write.XStringViews	XStringSet-io
writeFASTA	readFASTA
XInteger	Biostrings-internals
XInteger-class	Biostrings-internals
XRaw	Biostrings-internals
XRaw-class	Biostrings-internals
XString	XString-class
XString,AsIs-method	XString-class
XString,character-method	XString-class
XString,MaskedXString-method	MaskedXString-class
XString,XString-method	XString-class
XString-class	XString-class
XStringAlign	XStringAlign-class
XStringAlign-class	XStringAlign-class
XStringCodec	Biostrings-internals
XStringCodec-class	Biostrings-internals
XStringList	XStringSet-class
XStringList-class	XStringSet-class
XStringPartialMatches-class	XStringPartialMatches-class
XStringSet	XStringSet-class
XStringSet,AsIs-method	XStringSet-class
XStringSet,character-method	XStringSet-class
XStringSet,XString-method	XStringSet-class
XStringSet,XStringSet-method	XStringSet-class
XStringSet,XStringViews-method	XStringSet-class
XStringSet-class	XStringSet-class
XStringSetToFASTArecords	XStringSet-io
XStringViews	XStringViews-constructors
XStringViews,ANY-method	XStringViews-constructors
XStringViews,file-method	XStringViews-constructors
XStringViews,XString-method	XStringViews-constructors
XStringViews,XStringViews-method	XStringViews-constructors
XStringViews-class	XStringViews-class
XStringViews-constructors	XStringViews-constructors
yeastSEQCHR1	yeastSEQCHR1
[,ACtree-method	PDict-class
[,IRanges-method	IRanges-class
[,MaskCollection-method	MaskCollection-class
[,PrintableXRaw-method	Biostrings-internals
[,XInteger-method	Biostrings-internals
[,XRaw-method	Biostrings-internals
[,XString-method	XString-class
[,XStringList-method	XStringSet-class
[,XStringPartialMatches-method	XStringPartialMatches-class
[<-,IRanges-method	IRanges-class
[<-,MaskCollection-method	MaskCollection-class
[<-,XInteger-method	Biostrings-internals
[<-,XRaw-method	Biostrings-internals
[<-,XString-method	XString-class
[<-,XStringList-method	XStringSet-class
[[,ByName_MIndex-method	matchPDict-exact
[[,ByPos_MIndex-method	matchPDict-exact
[[,MaskCollection-method	MaskCollection-class
[[,MIndex-method	matchPDict-exact
[[,SparseList-method	Biostrings-internals
[[,XStringList-method	XStringSet-class
[[,XStringSet-method	XStringSet-class
[[,XStringViews-method	XStringViews-class
[[<-,MaskCollection-method	MaskCollection-class
[[<-,XStringList-method	XStringSet-class
[[<-,XStringSet-method	XStringSet-class
[[<-,XStringViews-method	XStringViews-class
