!=,BString,character-method	XString-class
!=,character,BString-method	XString-class
!=,character,XStringViews-method	XStringViews-class
!=,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
%in%,character,XStringSet-method	XStringSet-class
%in%,XString,XStringSet-method	XStringSet-class
%in%,XStringSet,XStringSet-method	XStringSet-class
.inplaceReplaceLetterAt	replaceLetterAt
==,BString,character-method	XString-class
==,character,BString-method	XString-class
==,character,XStringViews-method	XStringViews-class
==,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
AAKeySortedData	XKeySortedData
AAKeySortedData-class	XKeySortedData
AAKeySortedDataList	XKeySortedDataList
AAKeySortedDataList-class	XKeySortedDataList
AAString	AAString-class
AAString-class	AAString-class
AAStringSet	XStringSet-class
AAStringSet-class	XStringSet-class
AAStringSetList	XStringSetList-class
AAStringSetList-class	XStringSetList-class
AA_ALPHABET	AAString-class
AA_WCP	WCP
AA_WCP-class	WCP
ACtree2	PDict-class
ACtree2-class	PDict-class
adjacentViews	XStringViews-constructors
align-utils	align-utils
aligned	AlignedXStringSet-class
aligned,AlignedXStringSet0-method	AlignedXStringSet-class
aligned,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
AlignedXStringSet	AlignedXStringSet-class
AlignedXStringSet-class	AlignedXStringSet-class
AlignedXStringSet0	AlignedXStringSet-class
AlignedXStringSet0-class	AlignedXStringSet-class
alphabet	XString-class
alphabet,ANY-method	XString-class
alphabetFrequency	letterFrequency
alphabetFrequency,DNAString-method	letterFrequency
alphabetFrequency,DNAStringSet-method	letterFrequency
alphabetFrequency,MaskedXString-method	letterFrequency
alphabetFrequency,RNAString-method	letterFrequency
alphabetFrequency,RNAStringSet-method	letterFrequency
alphabetFrequency,XString-method	letterFrequency
alphabetFrequency,XStringSet-method	letterFrequency
alphabetFrequency,XStringViews-method	letterFrequency
AMINO_ACID_CODE	AMINO_ACID_CODE
append,QualityScaledXStringSet,QualityScaledXStringSet-method	QualityScaledXStringSet-class
as.character,AlignedXStringSet0-method	AlignedXStringSet-class
as.character,MaskedXString-method	MaskedXString-class
as.character,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
as.character,XString-method	XString-class
as.character,XStringSet-method	XStringSet-class
as.character,XStringViews-method	XStringViews-class
as.complex,DNAString-method	toComplex
as.integer,PhredQuality-method	XStringQuality-class
as.integer,SolexaQuality-method	XStringQuality-class
as.list,MTB_PDict-method	PDict-class
as.list,SparseList-method	Biostrings-internals
as.matrix,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
as.matrix,XStringSet-method	XStringSet-class
as.matrix,XStringViews-method	XStringViews-class
as.numeric,PhredQuality-method	XStringQuality-class
as.numeric,SolexaQuality-method	XStringQuality-class
basecontent	basecontent
BKeySortedData	XKeySortedData
BKeySortedData-class	XKeySortedData
BKeySortedDataList	XKeySortedDataList
BKeySortedDataList-class	XKeySortedDataList
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
BStringSet	XStringSet-class
BStringSet-class	XStringSet-class
BStringSetList	XStringSetList-class
BStringSetList-class	XStringSetList-class
BStringViews	XStringViews-constructors
BStringViews,ANY-method	XStringViews-constructors
BStringViews,file-method	XStringViews-constructors
BStringViews,XString-method	XStringViews-constructors
BStringViews,XStringViews-method	XStringViews-constructors
ByPos_MIndex-class	MIndex-class
B_WCP	WCP
B_WCP-class	WCP
cDNA	translate
CharacterToFASTArecords	XStringSet-io
chartr,ANY,ANY,MaskedXString-method	chartr
chartr,ANY,ANY,XString-method	chartr
chartr,ANY,ANY,XStringSet-method	chartr
chartr,ANY,ANY,XStringViews-method	chartr
class:AAKeySortedData	XKeySortedData
class:AAKeySortedDataList	XKeySortedDataList
class:AAString	AAString-class
class:AAStringSet	XStringSet-class
class:AAStringSetList	XStringSetList-class
class:AA_WCP	WCP
class:ACtree2	PDict-class
class:AlignedXStringSet	AlignedXStringSet-class
class:AlignedXStringSet0	AlignedXStringSet-class
class:BKeySortedData	XKeySortedData
class:BKeySortedDataList	XKeySortedDataList
class:BOC2_SubjectString	BOC_SubjectString-class
class:BOC_SubjectString	BOC_SubjectString-class
class:BString	XString-class
class:BStringSet	XStringSet-class
class:BStringSetList	XStringSetList-class
class:ByPos_MIndex	MIndex-class
class:B_WCP	WCP
class:DNAKeySortedData	XKeySortedData
class:DNAKeySortedDataList	XKeySortedDataList
class:DNAString	DNAString-class
class:DNAStringSet	XStringSet-class
class:DNAStringSetList	XStringSetList-class
class:DNA_WCP	WCP
class:Expanded_TB_PDict	PDict-class
class:InDel	InDel-class
class:MaskedAAString	MaskedXString-class
class:MaskedBString	MaskedXString-class
class:MaskedDNAString	MaskedXString-class
class:MaskedRNAString	MaskedXString-class
class:MaskedXString	MaskedXString-class
class:MIndex	MIndex-class
class:MTB_PDict	PDict-class
class:PairwiseAlignedFixedSubject	PairwiseAlignedXStringSet-class
class:PairwiseAlignedFixedSubjectSummary	PairwiseAlignedXStringSet-class
class:PairwiseAlignedXStringSet	PairwiseAlignedXStringSet-class
class:PDict	PDict-class
class:PDict3Parts	PDict-class
class:PhredQuality	XStringQuality-class
class:PreprocessedTB	PDict-class
class:QualityAlignedXStringSet	AlignedXStringSet-class
class:QualityScaledAAStringSet	QualityScaledXStringSet-class
class:QualityScaledBStringSet	QualityScaledXStringSet-class
class:QualityScaledDNAStringSet	QualityScaledXStringSet-class
class:QualityScaledRNAStringSet	QualityScaledXStringSet-class
class:QualityScaledXStringSet	QualityScaledXStringSet-class
class:RNAKeySortedData	XKeySortedData
class:RNAKeySortedDataList	XKeySortedDataList
class:RNAString	RNAString-class
class:RNAStringSet	XStringSet-class
class:RNAStringSetList	XStringSetList-class
class:RNA_WCP	WCP
class:SolexaQuality	XStringQuality-class
class:SparseList	Biostrings-internals
class:TB_PDict	PDict-class
class:Twobit	PDict-class
class:WCP	WCP
class:XKeySortedData	XKeySortedData
class:XKeySortedDataList	XKeySortedDataList
class:XString	XString-class
class:XStringCodec	Biostrings-internals
class:XStringPartialMatches	XStringPartialMatches-class
class:XStringQuality	XStringQuality-class
class:XStringSet	XStringSet-class
class:XStringSetList	XStringSetList-class
class:XStringViews	XStringViews-class
codons	translate
codons,DNAString-method	translate
codons,MaskedDNAString-method	translate
codons,MaskedRNAString-method	translate
codons,RNAString-method	translate
coerce,AAString,MaskedAAString-method	MaskedXString-class
coerce,BString,MaskedBString-method	MaskedXString-class
coerce,BString,PhredQuality-method	XStringQuality-class
coerce,BString,SolexaQuality-method	XStringQuality-class
coerce,BStringSet,PhredQuality-method	XStringQuality-class
coerce,BStringSet,SolexaQuality-method	XStringQuality-class
coerce,character,AAString-method	XString-class
coerce,character,AAStringSet-method	XStringSet-class
coerce,character,BString-method	XString-class
coerce,character,BStringSet-method	XStringSet-class
coerce,character,DNAString-method	XString-class
coerce,character,DNAStringSet-method	XStringSet-class
coerce,character,PhredQuality-method	XStringQuality-class
coerce,character,RNAString-method	XString-class
coerce,character,RNAStringSet-method	XStringSet-class
coerce,character,SolexaQuality-method	XStringQuality-class
coerce,character,XString-method	XString-class
coerce,character,XStringSet-method	XStringSet-class
coerce,DNAString,MaskedDNAString-method	MaskedXString-class
coerce,integer,PhredQuality-method	XStringQuality-class
coerce,integer,SolexaQuality-method	XStringQuality-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,MaskedAAString-method	MaskedXString-class
coerce,MaskedXString,MaskedBString-method	MaskedXString-class
coerce,MaskedXString,MaskedDNAString-method	MaskedXString-class
coerce,MaskedXString,MaskedRNAString-method	MaskedXString-class
coerce,MaskedXString,NormalIRanges-method	MaskedXString-class
coerce,MaskedXString,Views-method	MaskedXString-class
coerce,MaskedXString,XStringViews-method	MaskedXString-class
coerce,MIndex,CompressedIRangesList-method	MIndex-class
coerce,numeric,PhredQuality-method	XStringQuality-class
coerce,numeric,SolexaQuality-method	XStringQuality-class
coerce,PhredQuality,integer-method	XStringQuality-class
coerce,PhredQuality,numeric-method	XStringQuality-class
coerce,RNAString,MaskedRNAString-method	MaskedXString-class
coerce,SolexaQuality,integer-method	XStringQuality-class
coerce,SolexaQuality,numeric-method	XStringQuality-class
coerce,XString,AAString-method	XString-class
coerce,XString,AAStringSet-method	XStringSet-class
coerce,XString,BString-method	XString-class
coerce,XString,BStringSet-method	XStringSet-class
coerce,XString,DNAString-method	XString-class
coerce,XString,DNAStringSet-method	XStringSet-class
coerce,XString,RNAString-method	XString-class
coerce,XString,RNAStringSet-method	XStringSet-class
coerce,XString,XStringSet-method	XStringSet-class
coerce,XStringSet,AAStringSet-method	XStringSet-class
coerce,XStringSet,BStringSet-method	XStringSet-class
coerce,XStringSet,DNAStringSet-method	XStringSet-class
coerce,XStringSet,RNAStringSet-method	XStringSet-class
coerce,XStringViews,AAStringSet-method	XStringViews-class
coerce,XStringViews,BStringSet-method	XStringViews-class
coerce,XStringViews,DNAStringSet-method	XStringViews-class
coerce,XStringViews,RNAStringSet-method	XStringViews-class
coerce,XStringViews,XStringSet-method	XStringViews-class
collapse,MaskedXString-method	MaskedXString-class
compact	XStringSet-class
compact,XStringSet-method	XStringSet-class
compareStrings	align-utils
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method	align-utils
compareStrings,character,character-method	align-utils
compareStrings,PairwiseAlignedXStringSet,missing-method	align-utils
compareStrings,XString,XString-method	align-utils
compareStrings,XStringSet,XStringSet-method	align-utils
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
complementSeq	complementSeq
computeAllFlinks	PDict-class
computeAllFlinks,ACtree2-method	PDict-class
connection-class	Biostrings-internals
consensusMatrix	letterFrequency
consensusMatrix,character-method	letterFrequency
consensusMatrix,list-method	letterFrequency
consensusMatrix,matrix-method	letterFrequency
consensusMatrix,PairwiseAlignedFixedSubject-method	align-utils
consensusMatrix,XStringSet-method	letterFrequency
consensusMatrix,XStringViews-method	letterFrequency
consensusString	letterFrequency
consensusString,ANY-method	letterFrequency
consensusString,BStringSet-method	letterFrequency
consensusString,DNAStringSet-method	letterFrequency
consensusString,matrix-method	letterFrequency
consensusString,RNAStringSet-method	letterFrequency
consensusString,XStringViews-method	letterFrequency
consmat	letterFrequency
consmat,ANY-method	letterFrequency
countbases	basecontent
countIndex	MIndex-class
countIndex,ByPos_MIndex-method	MIndex-class
countIndex,MIndex-method	MIndex-class
countPattern	matchPattern
countPattern,BOC2_SubjectString-method	BOC_SubjectString-class
countPattern,character-method	matchPattern
countPattern,MaskedXString-method	matchPattern
countPattern,XString-method	matchPattern
countPattern,XStringSet-method	matchPattern
countPattern,XStringViews-method	matchPattern
countPDict	matchPDict-exact
countPDict,MaskedXString-method	matchPDict-exact
countPDict,XString-method	matchPDict-exact
countPDict,XStringSet-method	matchPDict-exact
countPDict,XStringViews-method	matchPDict-exact
countPWM	matchPWM
countPWM,character-method	matchPWM
countPWM,DNAString-method	matchPWM
countPWM,MaskedDNAString-method	matchPWM
countPWM,XStringViews-method	matchPWM
countWCP	matchWCP
countWCP,character-method	matchWCP
countWCP,MaskedXString-method	matchWCP
countWCP,XString-method	matchWCP
countWCP,XStringViews-method	matchWCP
coverage,AlignedXStringSet0-method	align-utils
coverage,MaskedXString-method	match-utils
coverage,MIndex-method	match-utils
coverage,PairwiseAlignedFixedSubject-method	align-utils
coverage,PairwiseAlignedFixedSubjectSummary-method	align-utils
dataKey	XKeySortedData
dataKey,XKeySortedData-method	XKeySortedData
dataTable	XKeySortedData
dataTable,XKeySortedData-method	XKeySortedData
deletion	InDel-class
deletion,InDel-method	InDel-class
deletion,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
dim,XKeySortedData-method	XKeySortedData
dimnames,XKeySortedData-method	XKeySortedData
dinucleotideFrequency	nucleotideFrequency
dinucleotideFrequencyTest	dinucleotideFrequencyTest
dinucleotideFrequencyTest,DNAStringSet-method	dinucleotideFrequencyTest
dinucleotideFrequencyTest,RNAStringSet-method	dinucleotideFrequencyTest
dna2rna	translate
DNAKeySortedData	XKeySortedData
DNAKeySortedData-class	XKeySortedData
DNAKeySortedDataList	XKeySortedDataList
DNAKeySortedDataList-class	XKeySortedDataList
DNAString	DNAString-class
DNAString-class	DNAString-class
DNAStringSet	XStringSet-class
DNAStringSet-class	XStringSet-class
DNAStringSetList	XStringSetList-class
DNAStringSetList-class	XStringSetList-class
DNA_ALPHABET	DNAString-class
DNA_BASES	DNAString-class
DNA_WCP	WCP
DNA_WCP-class	WCP
duplicated,PDict-method	PDict-class
duplicated,PreprocessedTB-method	PDict-class
duplicated,XStringSet-method	XStringSet-class
elementLengths,MIndex-method	MIndex-class
end,AlignedXStringSet0-method	AlignedXStringSet-class
endIndex	MIndex-class
endIndex,ByPos_MIndex-method	MIndex-class
errorSubstitutionMatrices	substitution_matrices
Expanded_TB_PDict	PDict-class
Expanded_TB_PDict-class	PDict-class
extractAllMatches	matchPDict-exact
extractTranscripts	extractTranscripts
fasta.info	XStringSet-io
FASTArecordsToBStringViews	XStringSet-io
FASTArecordsToCharacter	XStringSet-io
FASTArecordsToXStringViews	XStringSet-io
fastq.geometry	XStringSet-io
file-class	Biostrings-internals
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
gaps,MaskedXString-method	MaskedXString-class
GENETIC_CODE	GENETIC_CODE
gregexpr2	gregexpr2
hasAllFlinks	PDict-class
hasAllFlinks,ACtree2-method	PDict-class
hasLetterAt	lowlevel-matching
hasOnlyBaseLetters	letterFrequency
hasOnlyBaseLetters,DNAString-method	letterFrequency
hasOnlyBaseLetters,DNAStringSet-method	letterFrequency
hasOnlyBaseLetters,MaskedXString-method	letterFrequency
hasOnlyBaseLetters,RNAString-method	letterFrequency
hasOnlyBaseLetters,RNAStringSet-method	letterFrequency
hasOnlyBaseLetters,XStringViews-method	letterFrequency
head,PDict3Parts-method	PDict-class
head,TB_PDict-method	PDict-class
HNF4alpha	HNF4alpha
InDel	InDel-class
indel	AlignedXStringSet-class
indel,AlignedXStringSet0-method	AlignedXStringSet-class
indel,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
InDel-class	InDel-class
initialize,ACtree2-method	PDict-class
initialize,BOC2_SubjectString-method	BOC_SubjectString-class
initialize,BOC_SubjectString-method	BOC_SubjectString-class
initialize,PreprocessedTB-method	PDict-class
initialize,Twobit-method	PDict-class
initialize,XStringCodec-method	Biostrings-internals
injectHardMask	injectHardMask
injectHardMask,MaskedXString-method	injectHardMask
injectHardMask,XStringViews-method	injectHardMask
insertion	InDel-class
insertion,InDel-method	InDel-class
insertion,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
intersect,XStringSet,XStringSet-method	XStringSet-class
is.unsorted,XStringSet-method	XStringSet-class
isMatching	lowlevel-matching
isMatchingAt	lowlevel-matching
isMatchingEndingAt	lowlevel-matching
isMatchingEndingAt,character-method	lowlevel-matching
isMatchingEndingAt,XString-method	lowlevel-matching
isMatchingEndingAt,XStringSet-method	lowlevel-matching
isMatchingStartingAt	lowlevel-matching
isMatchingStartingAt,character-method	lowlevel-matching
isMatchingStartingAt,XString-method	lowlevel-matching
isMatchingStartingAt,XStringSet-method	lowlevel-matching
IUPAC_CODE_MAP	IUPAC_CODE_MAP
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,AlignedXStringSet0-method	AlignedXStringSet-class
length,MaskedXString-method	MaskedXString-class
length,MIndex-method	MIndex-class
length,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
length,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
length,PDict-method	PDict-class
length,PDict3Parts-method	PDict-class
length,PreprocessedTB-method	PDict-class
length,SparseList-method	Biostrings-internals
length,XKeySortedData-method	XKeySortedData
length,XStringSetList-method	XStringSetList-class
letter	letter
letter,character-method	letter
letter,MaskedXString-method	letter
letter,XString-method	letter
letter,XStringViews-method	letter
letterFrequency	letterFrequency
letterFrequencyInSlidingView	letterFrequency
letterFrequencyInSlidingView,XString-method	letterFrequency
longestConsecutive	longestConsecutive
lowlevel-matching	lowlevel-matching
ls,SparseList-method	Biostrings-internals
mask	maskMotif
MaskedAAString	MaskedXString-class
MaskedAAString-class	MaskedXString-class
MaskedBString	MaskedXString-class
MaskedBString-class	MaskedXString-class
MaskedDNAString	MaskedXString-class
MaskedDNAString-class	MaskedXString-class
maskedratio,MaskedXString-method	MaskedXString-class
MaskedRNAString	MaskedXString-class
MaskedRNAString-class	MaskedXString-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,character,XStringSet-method	XStringSet-class
match,XString,XStringSet-method	XStringSet-class
match,XStringSet,XStringSet-method	XStringSet-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,XStringSet-method	matchPattern
matchPattern,XStringViews-method	matchPattern
matchPDict	matchPDict-exact
matchPDict,MaskedXString-method	matchPDict-exact
matchPDict,XString-method	matchPDict-exact
matchPDict,XStringSet-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
matchprobes	matchprobes
matchPWM	matchPWM
matchPWM,character-method	matchPWM
matchPWM,DNAString-method	matchPWM
matchPWM,MaskedDNAString-method	matchPWM
matchPWM,XStringViews-method	matchPWM
matchWCP	matchWCP
matchWCP,character-method	matchWCP
matchWCP,MaskedXString-method	matchWCP
matchWCP,XString-method	matchWCP
matchWCP,XStringViews-method	matchWCP
maxScore	matchPWM
maxScore,ANY-method	matchPWM
maxWeights	matchPWM
maxWeights,matrix-method	matchPWM
maxWeights,WCP-method	WCP
mergeIUPACLetters	IUPAC_CODE_MAP
MIndex	MIndex-class
MIndex-class	MIndex-class
minScore	matchPWM
minScore,ANY-method	matchPWM
minWeights	matchPWM
minWeights,matrix-method	matchPWM
misc	misc
mismatch	match-utils
mismatch,AlignedXStringSet0,missing-method	align-utils
mismatch,ANY,XStringViews-method	match-utils
mismatchSummary	align-utils
mismatchSummary,AlignedXStringSet0-method	align-utils
mismatchSummary,PairwiseAlignedFixedSubject-method	align-utils
mismatchSummary,PairwiseAlignedFixedSubjectSummary-method	align-utils
mismatchSummary,QualityAlignedXStringSet-method	align-utils
mismatchTable	align-utils
mismatchTable,AlignedXStringSet0-method	align-utils
mismatchTable,PairwiseAlignedXStringSet-method	align-utils
mismatchTable,QualityAlignedXStringSet-method	align-utils
mkAllStrings	nucleotideFrequency
MTB_PDict	PDict-class
MTB_PDict-class	PDict-class
N50	misc
names,MIndex-method	MIndex-class
names,PDict-method	PDict-class
names,XStringSetList-method	XStringSetList-class
names<-,MIndex-method	MIndex-class
names<-,PDict-method	PDict-class
names<-,XStringSetList-method	XStringSetList-class
narrow,character-method	XStringSet-class
narrow,QualityScaledXStringSet-method	QualityScaledXStringSet-class
nchar,AlignedXStringSet0-method	AlignedXStringSet-class
nchar,MaskedXString-method	MaskedXString-class
nchar,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
nchar,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
nchar,XString-method	XString-class
nchar,XStringSet-method	XStringSet-class
nchar,XStringViews-method	XStringViews-class
nedit	align-utils
nedit,PairwiseAlignedFixedSubjectSummary-method	align-utils
nedit,PairwiseAlignedXStringSet-method	align-utils
neditAt	lowlevel-matching
neditEndingAt	lowlevel-matching
neditEndingAt,character-method	lowlevel-matching
neditEndingAt,XString-method	lowlevel-matching
neditEndingAt,XStringSet-method	lowlevel-matching
neditStartingAt	lowlevel-matching
neditStartingAt,character-method	lowlevel-matching
neditStartingAt,XString-method	lowlevel-matching
neditStartingAt,XStringSet-method	lowlevel-matching
needwunsQS	needwunsQS
needwunsQS,character,character-method	needwunsQS
needwunsQS,character,XString-method	needwunsQS
needwunsQS,XString,character-method	needwunsQS
needwunsQS,XString,XString-method	needwunsQS
nindel	AlignedXStringSet-class
nindel,AlignedXStringSet0-method	AlignedXStringSet-class
nindel,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
nindel,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
nmatch	match-utils
nmatch,ANY,XStringViews-method	match-utils
nmatch,PairwiseAlignedFixedSubjectSummary,missing-method	align-utils
nmatch,PairwiseAlignedXStringSet,missing-method	align-utils
nmismatch	match-utils
nmismatch,AlignedXStringSet0,missing-method	align-utils
nmismatch,ANY,XStringViews-method	match-utils
nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method	align-utils
nmismatch,PairwiseAlignedXStringSet,missing-method	align-utils
nmismatchEndingAt	lowlevel-matching
nmismatchStartingAt	lowlevel-matching
nnodes	PDict-class
nnodes,ACtree2-method	PDict-class
nucleotideFrequencyAt	nucleotideFrequency
nucleotideFrequencyAt,XStringSet-method	nucleotideFrequency
nucleotideFrequencyAt,XStringViews-method	nucleotideFrequency
nucleotideSubstitutionMatrix	substitution_matrices
oligonucleotideFrequency	nucleotideFrequency
oligonucleotideFrequency,MaskedXString-method	nucleotideFrequency
oligonucleotideFrequency,XString-method	nucleotideFrequency
oligonucleotideFrequency,XStringSet-method	nucleotideFrequency
oligonucleotideFrequency,XStringViews-method	nucleotideFrequency
oligonucleotideTransitions	nucleotideFrequency
order,XStringSet-method	XStringSet-class
PairwiseAlignedFixedSubject	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubject,character,character-method	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubject,character,missing-method	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubject,XString,XString-method	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubject,XStringSet,missing-method	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubject-class	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubjectSummary	PairwiseAlignedXStringSet-class
PairwiseAlignedFixedSubjectSummary-class	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet,character,character-method	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet,character,missing-method	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet,XString,XString-method	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet,XStringSet,missing-method	PairwiseAlignedXStringSet-class
PairwiseAlignedXStringSet-class	PairwiseAlignedXStringSet-class
pairwiseAlignment	pairwiseAlignment
pairwiseAlignment,character,character-method	pairwiseAlignment
pairwiseAlignment,character,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,character,XString-method	pairwiseAlignment
pairwiseAlignment,character,XStringSet-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,character-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,XString-method	pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,XStringSet-method	pairwiseAlignment
pairwiseAlignment,XString,character-method	pairwiseAlignment
pairwiseAlignment,XString,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,XString,XString-method	pairwiseAlignment
pairwiseAlignment,XString,XStringSet-method	pairwiseAlignment
pairwiseAlignment,XStringSet,character-method	pairwiseAlignment
pairwiseAlignment,XStringSet,QualityScaledXStringSet-method	pairwiseAlignment
pairwiseAlignment,XStringSet,XString-method	pairwiseAlignment
pairwiseAlignment,XStringSet,XStringSet-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
partitioning	XStringSetList-class
partitioning,XStringSetList-method	XStringSetList-class
pattern	XStringPartialMatches-class
pattern,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
pattern,XStringPartialMatches-method	XStringPartialMatches-class
patternFrequency	PDict-class
patternFrequency,PDict-method	PDict-class
PDict	PDict-class
PDict,AsIs-method	PDict-class
PDict,character-method	PDict-class
PDict,DNAStringSet-method	PDict-class
PDict,probetable-method	PDict-class
PDict,XStringViews-method	PDict-class
PDict-class	PDict-class
PDict3Parts	PDict-class
PDict3Parts-class	PDict-class
phiX174Phage	phiX174Phage
PhredQuality	XStringQuality-class
PhredQuality-class	XStringQuality-class
pid	pid
pid,PairwiseAlignedXStringSet-method	pid
pmatchPattern	pmatchPattern
pmatchPattern,character-method	pmatchPattern
pmatchPattern,XString-method	pmatchPattern
pmatchPattern,XStringViews-method	pmatchPattern
PreprocessedTB	PDict-class
PreprocessedTB-class	PDict-class
print.needwunsQS	needwunsQS
PWM	matchPWM
PWM,character-method	matchPWM
PWM,DNAStringSet-method	matchPWM
PWMscore	matchPWM
PWMscoreStartingAt	matchPWM
quality	QualityScaledXStringSet-class
quality,QualityScaledXStringSet-method	QualityScaledXStringSet-class
QualityAlignedXStringSet	AlignedXStringSet-class
QualityAlignedXStringSet-class	AlignedXStringSet-class
QualityScaledAAStringSet	QualityScaledXStringSet-class
QualityScaledAAStringSet-class	QualityScaledXStringSet-class
QualityScaledBStringSet	QualityScaledXStringSet-class
QualityScaledBStringSet-class	QualityScaledXStringSet-class
QualityScaledDNAStringSet	QualityScaledXStringSet-class
QualityScaledDNAStringSet-class	QualityScaledXStringSet-class
QualityScaledRNAStringSet	QualityScaledXStringSet-class
QualityScaledRNAStringSet-class	QualityScaledXStringSet-class
QualityScaledXStringSet	QualityScaledXStringSet-class
QualityScaledXStringSet-class	QualityScaledXStringSet-class
qualitySubstitutionMatrices	substitution_matrices
quPhiX174	phiX174Phage
rank,XStringSet-method	XStringSet-class
read.AAStringSet	XStringSet-io
read.BStringSet	XStringSet-io
read.BStringViews	XStringSet-io
read.DNAStringSet	XStringSet-io
read.RNAStringSet	XStringSet-io
read.XStringViews	XStringSet-io
readFASTA	readFASTA
rep,AlignedXStringSet0-method	AlignedXStringSet-class
rep,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
replaceLetterAt	replaceLetterAt
replaceLetterAt,DNAString-method	replaceLetterAt
replaceLetterAt,DNAStringSet-method	replaceLetterAt
replaceLetterAtLoc	replaceLetterAt
revcompDNA	reverseSeq
revcompRNA	reverseSeq
reverse,character-method	reverse
reverse,MaskedXString-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
reverseSeq	reverseSeq
rna2dna	translate
RNAKeySortedData	XKeySortedData
RNAKeySortedData-class	XKeySortedData
RNAKeySortedDataList	XKeySortedDataList
RNAKeySortedDataList-class	XKeySortedDataList
RNAString	RNAString-class
RNAString-class	RNAString-class
RNAStringSet	XStringSet-class
RNAStringSet-class	XStringSet-class
RNAStringSetList	XStringSetList-class
RNAStringSetList-class	XStringSetList-class
RNA_ALPHABET	RNAString-class
RNA_BASES	RNAString-class
RNA_GENETIC_CODE	GENETIC_CODE
RNA_WCP	WCP
RNA_WCP-class	WCP
save.XStringSet	XStringSet-io
score,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
score,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
setdiff,XStringSet,XStringSet-method	XStringSet-class
setequal,XStringSet,XStringSet-method	XStringSet-class
show,ACtree2-method	PDict-class
show,AlignedXStringSet0-method	AlignedXStringSet-class
show,ByPos_MIndex-method	MIndex-class
show,MaskedXString-method	MaskedXString-class
show,MTB_PDict-method	PDict-class
show,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
show,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
show,QualityScaledXStringSet-method	QualityScaledXStringSet-class
show,TB_PDict-method	PDict-class
show,Twobit-method	PDict-class
show,WCP-method	WCP
show,XString-method	XString-class
show,XStringPartialMatches-method	XStringPartialMatches-class
show,XStringSet-method	XStringSet-class
show,XStringSetList-method	XStringSetList-class
show,XStringViews-method	XStringViews-class
SolexaQuality	XStringQuality-class
SolexaQuality-class	XStringQuality-class
sort,XStringSet-method	XStringSet-class
SparseList	Biostrings-internals
SparseList-class	Biostrings-internals
srPhiX174	phiX174Phage
start,AlignedXStringSet0-method	AlignedXStringSet-class
startIndex	MIndex-class
startIndex,ByPos_MIndex-method	MIndex-class
stringDist	stringDist
stringDist,character-method	stringDist
stringDist,QualityScaledXStringSet-method	stringDist
stringDist,XStringSet-method	stringDist
strrev	reverse
subBString	subXString
subject,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
subpatterns	XStringPartialMatches-class
subpatterns,XStringPartialMatches-method	XStringPartialMatches-class
subseq,character-method	XStringSet-class
subseq,MaskedXString-method	MaskedXString-class
subseq<-,character-method	XStringSet-class
subseq<-,XStringSet-method	XStringSet-class
substitution.matrices	substitution_matrices
substr,MaskedXString-method	subXString
substr,XString-method	subXString
substring,MaskedXString-method	subXString
substring,XString-method	subXString
subXString	subXString
summary,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
tail,PDict3Parts-method	PDict-class
tail,TB_PDict-method	PDict-class
tb	PDict-class
tb,PDict3Parts-method	PDict-class
tb,PreprocessedTB-method	PDict-class
tb,TB_PDict-method	PDict-class
tb.width	PDict-class
tb.width,PDict3Parts-method	PDict-class
tb.width,PreprocessedTB-method	PDict-class
tb.width,TB_PDict-method	PDict-class
TB_PDict	PDict-class
TB_PDict-class	PDict-class
threebands,character-method	XStringSet-class
toComplex	toComplex
toComplex,DNAString-method	toComplex
toString,AlignedXStringSet0-method	AlignedXStringSet-class
toString,MaskedXString-method	MaskedXString-class
toString,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
toString,XString-method	XString-class
toString,XStringSet-method	XStringSet-class
toString,XStringViews-method	XStringViews-class
transcribe	translate
transcriptLocs2refLocs	extractTranscripts
transcriptWidths	extractTranscripts
translate	translate
translate,DNAString-method	translate
translate,DNAStringSet-method	translate
translate,MaskedDNAString-method	translate
translate,MaskedRNAString-method	translate
translate,RNAString-method	translate
translate,RNAStringSet-method	translate
trimLRPatterns	trimLRPatterns
trimLRPatterns,character-method	trimLRPatterns
trimLRPatterns,XString-method	trimLRPatterns
trimLRPatterns,XStringSet-method	trimLRPatterns
trinucleotideFrequency	nucleotideFrequency
Twobit	PDict-class
Twobit-class	PDict-class
type	PairwiseAlignedXStringSet-class
type,PairwiseAlignedFixedSubjectSummary-method	PairwiseAlignedXStringSet-class
type,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
unaligned	AlignedXStringSet-class
unaligned,AlignedXStringSet0-method	AlignedXStringSet-class
union,XStringSet,XStringSet-method	XStringSet-class
unique,XStringSet-method	XStringSet-class
uniqueLetters	letterFrequency
uniqueLetters,MaskedXString-method	letterFrequency
uniqueLetters,XString-method	letterFrequency
uniqueLetters,XStringSet-method	letterFrequency
uniqueLetters,XStringViews-method	letterFrequency
unitScale	matchPWM
unlist,MIndex-method	MIndex-class
unlist,XStringSet-method	XStringSet-class
unlist,XStringSetList-method	XStringSetList-class
unmasked	MaskedXString-class
unmasked,MaskedXString-method	MaskedXString-class
unsplit.list.of.XStringSet	XStringSet-class
updateObject,XString-method	XString-class
updateObject,XStringSet-method	XStringSet-class
vcountPattern	matchPattern
vcountPattern,character-method	matchPattern
vcountPattern,MaskedXString-method	matchPattern
vcountPattern,XString-method	matchPattern
vcountPattern,XStringSet-method	matchPattern
vcountPattern,XStringViews-method	matchPattern
vcountPDict	matchPDict-exact
vcountPDict,MaskedXString-method	matchPDict-exact
vcountPDict,XString-method	matchPDict-exact
vcountPDict,XStringSet-method	matchPDict-exact
vcountPDict,XStringViews-method	matchPDict-exact
Views,character-method	XStringViews-class
Views,MaskedXString-method	MaskedXString-class
Views,PairwiseAlignedFixedSubject-method	PairwiseAlignedXStringSet-class
Views,XString-method	XStringViews-class
vmatchPattern	matchPattern
vmatchPattern,character-method	matchPattern
vmatchPattern,MaskedXString-method	matchPattern
vmatchPattern,XString-method	matchPattern
vmatchPattern,XStringSet-method	matchPattern
vmatchPattern,XStringViews-method	matchPattern
vmatchPDict	matchPDict-exact
vmatchPDict,ANY-method	matchPDict-exact
vmatchPDict,MaskedXString-method	matchPDict-exact
vmatchPDict,XString-method	matchPDict-exact
vwhichPDict	matchPDict-exact
vwhichPDict,MaskedXString-method	matchPDict-exact
vwhichPDict,XString-method	matchPDict-exact
vwhichPDict,XStringSet-method	matchPDict-exact
vwhichPDict,XStringViews-method	matchPDict-exact
WCP	WCP
WCP-class	WCP
WCPscoreStartingAt	matchWCP
which.isMatchingAt	lowlevel-matching
which.isMatchingEndingAt	lowlevel-matching
which.isMatchingEndingAt,character-method	lowlevel-matching
which.isMatchingEndingAt,XString-method	lowlevel-matching
which.isMatchingEndingAt,XStringSet-method	lowlevel-matching
which.isMatchingStartingAt	lowlevel-matching
which.isMatchingStartingAt,character-method	lowlevel-matching
which.isMatchingStartingAt,XString-method	lowlevel-matching
which.isMatchingStartingAt,XStringSet-method	lowlevel-matching
whichPDict	matchPDict-exact
whichPDict,MaskedXString-method	matchPDict-exact
whichPDict,XString-method	matchPDict-exact
whichPDict,XStringSet-method	matchPDict-exact
whichPDict,XStringViews-method	matchPDict-exact
width,AlignedXStringSet0-method	AlignedXStringSet-class
width,character-method	XStringSet-class
width,PDict-method	PDict-class
width,PDict3Parts-method	PDict-class
width,PreprocessedTB-method	PDict-class
width0	MIndex-class
width0,MIndex-method	MIndex-class
write.BStringViews	XStringSet-io
write.XStringSet	XStringSet-io
write.XStringViews	XStringSet-io
writeFASTA	readFASTA
wtPhiX174	phiX174Phage
XKeySortedData	XKeySortedData
XKeySortedData-class	XKeySortedData
XKeySortedDataList	XKeySortedDataList
XKeySortedDataList-class	XKeySortedDataList
xsbasetype	Biostrings-internals
xsbasetype,AAString-method	XString-class
xsbasetype,AlignedXStringSet0-method	AlignedXStringSet-class
xsbasetype,BString-method	XString-class
xsbasetype,DNAString-method	XString-class
xsbasetype,MaskedXString-method	MaskedXString-class
xsbasetype,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
xsbasetype,RNAString-method	XString-class
xsbasetype,WCP-method	WCP
xsbasetype,XKeySortedData-method	XKeySortedData
xsbasetype,XKeySortedDataList-method	XKeySortedDataList
xsbasetype,XStringSet-method	XStringSet-class
xsbasetype,XStringSetList-method	XStringSetList-class
xsbasetype,XStringViews-method	XStringViews-class
xsbasetype<-	Biostrings-internals
xsbasetype<-,MaskedXString-method	MaskedXString-class
xsbasetype<-,XString-method	XString-class
xsbasetype<-,XStringSet-method	XStringSet-class
xsbasetype<-,XStringSetList-method	XStringSetList-class
xsbasetype<-,XStringViews-method	XStringViews-class
xscat	xscat
XString	XString-class
XString-class	XString-class
XStringCodec	Biostrings-internals
XStringCodec-class	Biostrings-internals
XStringPartialMatches-class	XStringPartialMatches-class
XStringQuality	XStringQuality-class
XStringQuality-class	XStringQuality-class
XStringSet	XStringSet-class
XStringSet-class	XStringSet-class
XStringSetList	XStringSetList-class
XStringSetList-class	XStringSetList-class
XStringSetToFASTArecords	XStringSet-io
XStringViews	XStringViews-constructors
XStringViews,ANY-method	XStringViews-constructors
XStringViews,XString-method	XStringViews-constructors
XStringViews,XStringViews-method	XStringViews-constructors
XStringViews-class	XStringViews-class
XStringViews-constructors	XStringViews-constructors
yeastSEQCHR1	yeastSEQCHR1
[,AlignedXStringSet0-method	AlignedXStringSet-class
[,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
[,QualityScaledXStringSet-method	QualityScaledXStringSet-class
[,XKeySortedData-method	XKeySortedData
[,XStringPartialMatches-method	XStringPartialMatches-class
[<-,AlignedXStringSet0-method	AlignedXStringSet-class
[<-,PairwiseAlignedXStringSet-method	PairwiseAlignedXStringSet-class
[[,ByPos_MIndex-method	MIndex-class
[[,PDict-method	PDict-class
[[,SparseList-method	Biostrings-internals
[[,XKeySortedData-method	XKeySortedData
[[,XStringSetList-method	XStringSetList-class
[[<-,XStringSetList-method	XStringSetList-class
