/usr/lib/R/site-library/Biostrings/help/AnIndex is in r-bioc-biostrings 2.32.1-1.
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!=,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
.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
AAMultipleAlignment MultipleAlignment-class
AAMultipleAlignment-class MultipleAlignment-class
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_PROTEINOGENIC AAString-class
AA_STANDARD AAString-class
ACtree2 PDict-class
ACtree2-class PDict-class
align-utils align-utils
aligned AlignedXStringSet-class
aligned,AlignedXStringSet0-method AlignedXStringSet-class
aligned,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-class
AlignedXStringSet AlignedXStringSet-class
AlignedXStringSet-class AlignedXStringSet-class
AlignedXStringSet0 AlignedXStringSet-class
AlignedXStringSet0-class AlignedXStringSet-class
alphabet XString-class
alphabet,ANY-method XString-class
alphabet,XStringQuality-method XStringQuality-class
alphabetFrequency letterFrequency
alphabetFrequency,AAString-method letterFrequency
alphabetFrequency,AAStringSet-method letterFrequency
alphabetFrequency,DNAString-method letterFrequency
alphabetFrequency,DNAStringSet-method letterFrequency
alphabetFrequency,MaskedXString-method letterFrequency
alphabetFrequency,MultipleAlignment-method MultipleAlignment-class
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,MultipleAlignment-method MultipleAlignment-class
as.character,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-class
as.character,XString-method XString-class
as.character,XStringSet-method XStringSet-class
as.character,XStringViews-method XStringViews-class
as.integer,IlluminaQuality-method XStringQuality-class
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,MultipleAlignment-method MultipleAlignment-class
as.matrix,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-class
as.matrix,XStringQuality-method XStringQuality-class
as.matrix,XStringSet-method XStringSet-class
as.matrix,XStringViews-method XStringViews-class
as.numeric,IlluminaQuality-method XStringQuality-class
as.numeric,PhredQuality-method XStringQuality-class
as.numeric,SolexaQuality-method XStringQuality-class
as.vector,XStringSet-method XStringSet-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
BStringSet XStringSet-class
BStringSet-class XStringSet-class
BStringSetList XStringSetList-class
BStringSetList-class XStringSetList-class
ByPos_MIndex-class MIndex-class
cDNA translate
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:AAMultipleAlignment MultipleAlignment-class
class:AAString AAString-class
class:AAStringSet XStringSet-class
class:AAStringSetList XStringSetList-class
class:ACtree2 PDict-class
class:AlignedXStringSet AlignedXStringSet-class
class:AlignedXStringSet0 AlignedXStringSet-class
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:DNAMultipleAlignment MultipleAlignment-class
class:DNAString DNAString-class
class:DNAStringSet XStringSet-class
class:DNAStringSetList XStringSetList-class
class:Expanded_TB_PDict PDict-class
class:IlluminaQuality XStringQuality-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:MultipleAlignment MultipleAlignment-class
class:PairwiseAlignments PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubject PairwiseAlignments-class
class:PairwiseAlignmentsSingleSubjectSummary PairwiseAlignments-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:RNAMultipleAlignment MultipleAlignment-class
class:RNAString RNAString-class
class:RNAStringSet XStringSet-class
class:RNAStringSetList XStringSetList-class
class:SolexaQuality XStringQuality-class
class:SparseList Biostrings-internals
class:TB_PDict PDict-class
class:Twobit PDict-class
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,ANY,AAStringSet-method XStringSet-class
coerce,ANY,BStringSet-method XStringSet-class
coerce,ANY,DNAStringSet-method XStringSet-class
coerce,ANY,RNAStringSet-method XStringSet-class
coerce,ANY,XStringSet-method XStringSet-class
coerce,BString,IlluminaQuality-method XStringQuality-class
coerce,BString,MaskedBString-method MaskedXString-class
coerce,BString,PhredQuality-method XStringQuality-class
coerce,BString,SolexaQuality-method XStringQuality-class
coerce,BStringSet,IlluminaQuality-method XStringQuality-class
coerce,BStringSet,PhredQuality-method XStringQuality-class
coerce,BStringSet,SolexaQuality-method XStringQuality-class
coerce,character,AAMultipleAlignment-method MultipleAlignment-class
coerce,character,AAString-method XString-class
coerce,character,BString-method XString-class
coerce,character,DNAMultipleAlignment-method MultipleAlignment-class
coerce,character,DNAString-method XString-class
coerce,character,IlluminaQuality-method XStringQuality-class
coerce,character,PhredQuality-method XStringQuality-class
coerce,character,RNAMultipleAlignment-method MultipleAlignment-class
coerce,character,RNAString-method XString-class
coerce,character,SolexaQuality-method XStringQuality-class
coerce,character,XString-method XString-class
coerce,DNAString,MaskedDNAString-method MaskedXString-class
coerce,IlluminaQuality,integer-method XStringQuality-class
coerce,IlluminaQuality,numeric-method XStringQuality-class
coerce,integer,IlluminaQuality-method XStringQuality-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,MultipleAlignment,AAStringSet-method MultipleAlignment-class
coerce,MultipleAlignment,BStringSet-method MultipleAlignment-class
coerce,MultipleAlignment,DNAStringSet-method MultipleAlignment-class
coerce,MultipleAlignment,RNAStringSet-method MultipleAlignment-class
coerce,numeric,IlluminaQuality-method XStringQuality-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,BString-method XString-class
coerce,XString,DNAString-method XString-class
coerce,XString,RNAString-method XString-class
coerce,XStringQuality,matrix-method XStringQuality-class
coerce,XStringSet,Views-method XStringViews-class
coerce,XStringSet,XStringViews-method XStringViews-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
colmask MultipleAlignment-class
colmask,MultipleAlignment-method MultipleAlignment-class
colmask<- MultipleAlignment-class
colmask<-,MultipleAlignment,ANY-method MultipleAlignment-class
colmask<-,MultipleAlignment,NormalIRanges-method MultipleAlignment-class
colmask<-,MultipleAlignment,NULL-method MultipleAlignment-class
compare,ANY,XStringSet-method XStringSet-comparison
compare,XStringSet,ANY-method XStringSet-comparison
compare,XStringSet,XStringSet-method XStringSet-comparison
compareStrings align-utils
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method align-utils
compareStrings,character,character-method align-utils
compareStrings,PairwiseAlignments,missing-method align-utils
compareStrings,XString,XString-method align-utils
compareStrings,XStringSet,XStringSet-method align-utils
complement reverseComplement
complement,DNAString-method reverseComplement
complement,DNAStringSet-method reverseComplement
complement,MaskedDNAString-method reverseComplement
complement,MaskedRNAString-method reverseComplement
complement,RNAString-method reverseComplement
complement,RNAStringSet-method reverseComplement
complement,XStringViews-method reverseComplement
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
computeAllFlinks PDict-class
computeAllFlinks,ACtree2-method PDict-class
consensusMatrix letterFrequency
consensusMatrix,character-method letterFrequency
consensusMatrix,matrix-method letterFrequency
consensusMatrix,MultipleAlignment-method MultipleAlignment-class
consensusMatrix,PairwiseAlignmentsSingleSubject-method align-utils
consensusMatrix,XStringSet-method letterFrequency
consensusMatrix,XStringViews-method letterFrequency
consensusString letterFrequency
consensusString,AAMultipleAlignment-method MultipleAlignment-class
consensusString,ANY-method letterFrequency
consensusString,BStringSet-method letterFrequency
consensusString,DNAMultipleAlignment-method MultipleAlignment-class
consensusString,DNAStringSet-method letterFrequency
consensusString,matrix-method letterFrequency
consensusString,MultipleAlignment-method MultipleAlignment-class
consensusString,RNAMultipleAlignment-method MultipleAlignment-class
consensusString,RNAStringSet-method letterFrequency
consensusString,XStringViews-method letterFrequency
consensusViews MultipleAlignment-class
consensusViews,AAMultipleAlignment-method MultipleAlignment-class
consensusViews,DNAMultipleAlignment-method MultipleAlignment-class
consensusViews,MultipleAlignment-method MultipleAlignment-class
consensusViews,RNAMultipleAlignment-method MultipleAlignment-class
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
coverage,AlignedXStringSet0-method align-utils
coverage,MaskedXString-method match-utils
coverage,MIndex-method match-utils
coverage,PairwiseAlignmentsSingleSubject-method align-utils
coverage,PairwiseAlignmentsSingleSubjectSummary-method align-utils
deletion InDel-class
deletion,InDel-method InDel-class
deletion,PairwiseAlignments-method PairwiseAlignments-class
detail detail
detail,MultipleAlignment-method MultipleAlignment-class
dim,MultipleAlignment-method MultipleAlignment-class
dinucleotideFrequency nucleotideFrequency
dinucleotideFrequencyTest dinucleotideFrequencyTest
dinucleotideFrequencyTest,DNAStringSet-method dinucleotideFrequencyTest
dinucleotideFrequencyTest,RNAStringSet-method dinucleotideFrequencyTest
dna2rna translate
DNAMultipleAlignment MultipleAlignment-class
DNAMultipleAlignment-class MultipleAlignment-class
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
duplicated,PDict-method PDict-class
duplicated,PreprocessedTB-method PDict-class
elementLengths,MIndex-method MIndex-class
encoding XStringQuality-class
encoding,XStringQuality-method XStringQuality-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
extractAt replaceAt
extractAt,XString-method replaceAt
extractAt,XStringSet-method replaceAt
fasta.info XStringSet-io
fastq.geometry 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
gaps,MaskedXString-method MaskedXString-class
GENETIC_CODE GENETIC_CODE
GENETIC_CODE_TABLE GENETIC_CODE
getGeneticCode GENETIC_CODE
getSeq getSeq
get_seqtype_conversion_lookup Biostrings-internals
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
IlluminaQuality XStringQuality-class
IlluminaQuality-class XStringQuality-class
InDel InDel-class
indel AlignedXStringSet-class
indel,AlignedXStringSet0-method AlignedXStringSet-class
indel,PairwiseAlignments-method PairwiseAlignments-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,PairwiseAlignments-method PairwiseAlignments-class
intersect,XStringSet,XStringSet-method XStringSet-class
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,PairwiseAlignments-method PairwiseAlignments-class
length,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
length,PDict-method PDict-class
length,PDict3Parts-method PDict-class
length,PreprocessedTB-method PDict-class
length,SparseList-method Biostrings-internals
letter letter
letter,character-method letter
letter,MaskedXString-method letter
letter,XString-method letter
letter,XStringViews-method letter
letterFrequency letterFrequency
letterFrequency,MaskedXString-method letterFrequency
letterFrequency,XString-method letterFrequency
letterFrequency,XStringSet-method letterFrequency
letterFrequency,XStringViews-method letterFrequency
letterFrequencyInSlidingView letterFrequency
letterFrequencyInSlidingView,XString-method letterFrequency
longestConsecutive longestConsecutive
lowlevel-matching lowlevel-matching
mask maskMotif
MaskedAAString MaskedXString-class
MaskedAAString-class MaskedXString-class
MaskedBString MaskedXString-class
MaskedBString-class MaskedXString-class
maskeddim MultipleAlignment-class
maskeddim,MultipleAlignment-method MultipleAlignment-class
MaskedDNAString MaskedXString-class
MaskedDNAString-class MaskedXString-class
maskedncol MultipleAlignment-class
maskedncol,MultipleAlignment-method MultipleAlignment-class
maskednrow MultipleAlignment-class
maskednrow,MultipleAlignment-method MultipleAlignment-class
maskedratio,MaskedXString-method MaskedXString-class
maskedratio,MultipleAlignment-method MultipleAlignment-class
MaskedRNAString MaskedXString-class
MaskedRNAString-class MaskedXString-class
maskedwidth,MaskedXString-method MaskedXString-class
MaskedXString MaskedXString-class
MaskedXString-class MaskedXString-class
maskGaps MultipleAlignment-class
maskGaps,MultipleAlignment-method MultipleAlignment-class
maskMotif maskMotif
maskMotif,MaskedXString,character-method maskMotif
maskMotif,MaskedXString,XString-method maskMotif
maskMotif,MultipleAlignment,ANY-method MultipleAlignment-class
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,ANY,XStringSet-method XStringSet-comparison
match,XStringSet,ANY-method XStringSet-comparison
match,XStringSet,XStringSet-method XStringSet-comparison
match-utils match-utils
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
maxScore matchPWM
maxScore,ANY-method matchPWM
maxWeights matchPWM
maxWeights,matrix-method matchPWM
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,PairwiseAlignmentsSingleSubject-method align-utils
mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method align-utils
mismatchSummary,QualityAlignedXStringSet-method align-utils
mismatchTable align-utils
mismatchTable,AlignedXStringSet0-method align-utils
mismatchTable,PairwiseAlignments-method align-utils
mismatchTable,QualityAlignedXStringSet-method align-utils
mkAllStrings nucleotideFrequency
MTB_PDict PDict-class
MTB_PDict-class PDict-class
MultipleAlignment MultipleAlignment-class
MultipleAlignment-class MultipleAlignment-class
N50 misc
names,MIndex-method MIndex-class
names,PDict-method PDict-class
names<-,MIndex-method MIndex-class
names<-,PDict-method PDict-class
narrow,character-method XStringSet-class
narrow,QualityScaledXStringSet-method QualityScaledXStringSet-class
nchar,AlignedXStringSet0-method AlignedXStringSet-class
nchar,MaskedXString-method MaskedXString-class
nchar,MultipleAlignment-method MultipleAlignment-class
nchar,PairwiseAlignments-method PairwiseAlignments-class
nchar,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
nchar,XString-method XString-class
nchar,XStringSet-method XStringSet-class
nchar,XStringSetList-method XStringSetList-class
nchar,XStringViews-method XStringViews-class
ncol,MultipleAlignment-method MultipleAlignment-class
nedit align-utils
nedit,PairwiseAlignments-method align-utils
nedit,PairwiseAlignmentsSingleSubjectSummary-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,PairwiseAlignments-method PairwiseAlignments-class
nindel,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
nmatch match-utils
nmatch,ANY,XStringViews-method match-utils
nmatch,PairwiseAlignments,missing-method align-utils
nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method align-utils
nmismatch match-utils
nmismatch,AlignedXStringSet0,missing-method align-utils
nmismatch,ANY,XStringViews-method match-utils
nmismatch,PairwiseAlignments,missing-method align-utils
nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method align-utils
nnodes PDict-class
nnodes,ACtree2-method PDict-class
nrow,MultipleAlignment-method MultipleAlignment-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
padAndClip padAndClip
pairwiseAlignment pairwiseAlignment
pairwiseAlignment,ANY,ANY-method pairwiseAlignment
pairwiseAlignment,ANY,QualityScaledXStringSet-method pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,ANY-method pairwiseAlignment
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method pairwiseAlignment
PairwiseAlignments PairwiseAlignments-class
PairwiseAlignments,character,character-method PairwiseAlignments-class
PairwiseAlignments,character,missing-method PairwiseAlignments-class
PairwiseAlignments,XString,XString-method PairwiseAlignments-class
PairwiseAlignments,XStringSet,missing-method PairwiseAlignments-class
PairwiseAlignments-class PairwiseAlignments-class
PairwiseAlignments-io PairwiseAlignments-io
PairwiseAlignmentsSingleSubject PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,character,character-method PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,character,missing-method PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,XString,XString-method PairwiseAlignments-class
PairwiseAlignmentsSingleSubject,XStringSet,missing-method PairwiseAlignments-class
PairwiseAlignmentsSingleSubject-class PairwiseAlignments-class
PairwiseAlignmentsSingleSubjectSummary PairwiseAlignments-class
PairwiseAlignmentsSingleSubjectSummary-class PairwiseAlignments-class
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
pattern XStringPartialMatches-class
pattern,PairwiseAlignments-method PairwiseAlignments-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,PairwiseAlignments-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
PWM,matrix-method 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
readAAMultipleAlignment MultipleAlignment-class
readAAStringSet XStringSet-io
readBStringSet XStringSet-io
readDNAMultipleAlignment MultipleAlignment-class
readDNAStringSet XStringSet-io
readRNAMultipleAlignment MultipleAlignment-class
readRNAStringSet XStringSet-io
rep,AlignedXStringSet0-method AlignedXStringSet-class
rep,PairwiseAlignments-method PairwiseAlignments-class
replaceAt replaceAt
replaceAt,XString-method replaceAt
replaceAt,XStringSet-method replaceAt
replaceLetterAt replaceLetterAt
replaceLetterAt,DNAString-method replaceLetterAt
replaceLetterAt,DNAStringSet-method replaceLetterAt
reverse,MaskedXString-method reverseComplement
reverseComplement reverseComplement
reverseComplement,DNAString-method reverseComplement
reverseComplement,DNAStringSet-method reverseComplement
reverseComplement,MaskedDNAString-method reverseComplement
reverseComplement,MaskedRNAString-method reverseComplement
reverseComplement,matrix-method matchPWM
reverseComplement,RNAString-method reverseComplement
reverseComplement,RNAStringSet-method reverseComplement
reverseComplement,XStringViews-method reverseComplement
rna2dna translate
RNAMultipleAlignment MultipleAlignment-class
RNAMultipleAlignment-class MultipleAlignment-class
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
rowmask MultipleAlignment-class
rowmask,MultipleAlignment-method MultipleAlignment-class
rowmask<- MultipleAlignment-class
rowmask<-,MultipleAlignment,ANY-method MultipleAlignment-class
rowmask<-,MultipleAlignment,NormalIRanges-method MultipleAlignment-class
rowmask<-,MultipleAlignment,NULL-method MultipleAlignment-class
rownames,MultipleAlignment-method MultipleAlignment-class
rownames<-,MultipleAlignment-method MultipleAlignment-class
saveXStringSet XStringSet-io
score,PairwiseAlignments-method PairwiseAlignments-class
score,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
seqtype Biostrings-internals
seqtype,AAString-method XString-class
seqtype,AlignedXStringSet0-method AlignedXStringSet-class
seqtype,BString-method XString-class
seqtype,DNAString-method XString-class
seqtype,MaskedXString-method MaskedXString-class
seqtype,MultipleAlignment-method MultipleAlignment-class
seqtype,PairwiseAlignments-method PairwiseAlignments-class
seqtype,RNAString-method XString-class
seqtype,XStringSet-method XStringSet-class
seqtype,XStringSetList-method XStringSetList-class
seqtype,XStringViews-method XStringViews-class
seqtype<- Biostrings-internals
seqtype<-,MaskedXString-method MaskedXString-class
seqtype<-,XString-method XString-class
seqtype<-,XStringSet-method XStringSet-class
seqtype<-,XStringSetList-method XStringSetList-class
seqtype<-,XStringViews-method XStringViews-class
setdiff,XStringSet,XStringSet-method XStringSet-class
setequal,XStringSet,XStringSet-method XStringSet-class
show,ACtree2-method PDict-class
show,AlignedXStringSet0-method AlignedXStringSet-class
show,MaskedXString-method MaskedXString-class
show,MIndex-method MIndex-class
show,MTB_PDict-method PDict-class
show,MultipleAlignment-method MultipleAlignment-class
show,PairwiseAlignments-method PairwiseAlignments-class
show,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
show,QualityScaledXStringSet-method QualityScaledXStringSet-class
show,TB_PDict-method PDict-class
show,Twobit-method PDict-class
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
SparseList Biostrings-internals
SparseList-class Biostrings-internals
srPhiX174 phiX174Phage
stackStrings padAndClip
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
subject,PairwiseAlignments-method PairwiseAlignments-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,XString-method XString-class
substring,XString-method XString-class
summary,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-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,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-class
toString,XString-method XString-class
toString,XStringSet-method XStringSet-class
toString,XStringViews-method XStringViews-class
transcribe translate
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 PairwiseAlignments-class
type,PairwiseAlignments-method PairwiseAlignments-class
type,PairwiseAlignmentsSingleSubjectSummary-method PairwiseAlignments-class
unaligned AlignedXStringSet-class
unaligned,AlignedXStringSet0-method AlignedXStringSet-class
union,XStringSet,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
unmasked MaskedXString-class
unmasked,MaskedXString-method MaskedXString-class
unmasked,MultipleAlignment-method MultipleAlignment-class
unmasked,XString-method MaskedXString-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,PairwiseAlignmentsSingleSubject-method PairwiseAlignments-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
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.phylip MultipleAlignment-class
writePairwiseAlignments PairwiseAlignments-io
writeXStringSet XStringSet-io
wtPhiX174 phiX174Phage
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
XStringSet-comparison XStringSet-comparison
XStringSet-io XStringSet-io
XStringSetList XStringSetList-class
XStringSetList-class XStringSetList-class
XStringViews XStringViews-class
XStringViews-class XStringViews-class
yeastSEQCHR1 yeastSEQCHR1
[,AlignedXStringSet0-method AlignedXStringSet-class
[,PairwiseAlignments-method PairwiseAlignments-class
[,QualityScaledXStringSet-method QualityScaledXStringSet-class
[,XStringPartialMatches-method XStringPartialMatches-class
[<-,AlignedXStringSet0-method AlignedXStringSet-class
[<-,PairwiseAlignments-method PairwiseAlignments-class
[[,ByPos_MIndex-method MIndex-class
[[,PDict-method PDict-class
[[,SparseList-method Biostrings-internals
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