# String objects representing biological sequences, and matching algorithms

## Documentation for package ‘Biostrings’ version 2.14.12

## User Guides and Package Vignettes

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## Help Pages

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## -- --

!=,BString,character-method | BString objects
!=,character,BString-method | BString objects
!=,character,XStringViews-method | The XStringViews class
!=,XString,XString-method | BString objects
!=,XString,XStringViews-method | The XStringViews class
!=,XStringViews,character-method | The XStringViews class
!=,XStringViews,XString-method | The XStringViews class
!=,XStringViews,XStringViews-method | The XStringViews class
%in%,character,XStringSet-method | XStringSet objects
%in%,XString,XStringSet-method | XStringSet objects
%in%,XStringSet,XStringSet-method | XStringSet objects
.inplaceReplaceLetterAt | Replacing letters in a sequence (or set of sequences) at some specified locations
==,BString,character-method | BString objects
==,character,BString-method | BString objects
==,character,XStringViews-method | The XStringViews class
==,XString,XString-method | BString objects
==,XString,XStringViews-method | The XStringViews class
==,XStringViews,character-method | The XStringViews class
==,XStringViews,XString-method | The XStringViews class
==,XStringViews,XStringViews-method | The XStringViews class

## -- A --

AAKeySortedData | Data Dictionaries with XString-based Keys
AAKeySortedData-class | Data Dictionaries with XString-based Keys
AAKeySortedDataList | List of Data Dictionaries with XString-based Keys
AAKeySortedDataList-class | List of Data Dictionaries with XString-based Keys
AAString | AAString objects
AAString-class | AAString objects
AAStringSet | XStringSet objects
AAStringSet-class | XStringSet objects
AAStringSetList | XStringSetList objects
AAStringSetList-class | XStringSetList objects
AA_ALPHABET | AAString objects
AA_WCP | Weighted Clustered Positions (WCP) objects
AA_WCP-class | Weighted Clustered Positions (WCP) objects
ACtree | PDict objects
ACtree-class | PDict objects
ACtree2 | PDict objects
ACtree2-class | PDict objects
adjacentViews | Basic functions for creating or modifying XStringViews objects
align-utils | Utility functions related to sequence alignment
aligned | AlignedXStringSet and QualityAlignedXStringSet objects
aligned,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
aligned,PairwiseAlignedFixedSubject-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0-class | AlignedXStringSet and QualityAlignedXStringSet objects
alphabet | BString objects
alphabet,ANY-method | BString objects
alphabetFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,DNAString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,DNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,MaskedXString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,RNAString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,RNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,XString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,XStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency,XStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
AMINO_ACID_CODE | The Single-Letter Amino Acid Code
append,QualityScaledXStringSet,QualityScaledXStringSet-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
as.character,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
as.character,MaskedXString-method | MaskedXString objects
as.character,PairwiseAlignedFixedSubject-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
as.character,XString-method | BString objects
as.character,XStringSet-method | XStringSet objects
as.character,XStringViews-method | The XStringViews class
as.complex,DNAString-method | Turning a DNA sequence into a vector of complex numbers
as.integer,PhredQuality-method | PhredQuality and SolexaQuality objects
as.integer,SolexaQuality-method | PhredQuality and SolexaQuality objects
as.list,MTB_PDict-method | PDict objects
as.matrix,ACtree-method | PDict objects
as.matrix,PairwiseAlignedFixedSubject-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
as.matrix,XStringSet-method | XStringSet objects
as.matrix,XStringViews-method | The XStringViews class
as.numeric,PhredQuality-method | PhredQuality and SolexaQuality objects
as.numeric,SolexaQuality-method | PhredQuality and SolexaQuality objects

## -- B --

basecontent | Obtain the ATCG content of a gene
BKeySortedData | Data Dictionaries with XString-based Keys
BKeySortedData-class | Data Dictionaries with XString-based Keys
BKeySortedDataList | List of Data Dictionaries with XString-based Keys
BKeySortedDataList-class | List of Data Dictionaries with XString-based Keys
BLOSUM100 | Scoring matrices
BLOSUM45 | Scoring matrices
BLOSUM50 | Scoring matrices
BLOSUM62 | Scoring matrices
BLOSUM80 | Scoring matrices
BOC2_SubjectString | BOC\_SubjectString and BOC2\_SubjectString objects
BOC2_SubjectString-class | BOC\_SubjectString and BOC2\_SubjectString objects
BOC_SubjectString | BOC\_SubjectString and BOC2\_SubjectString objects
BOC_SubjectString-class | BOC\_SubjectString and BOC2\_SubjectString objects
BString | BString objects
BString-class | BString objects
BStringSet | XStringSet objects
BStringSet-class | XStringSet objects
BStringSetList | XStringSetList objects
BStringSetList-class | XStringSetList objects
BStringViews | Basic functions for creating or modifying XStringViews objects
BStringViews,ANY-method | Basic functions for creating or modifying XStringViews objects
BStringViews,file-method | Basic functions for creating or modifying XStringViews objects
BStringViews,XString-method | Basic functions for creating or modifying XStringViews objects
BStringViews,XStringViews-method | Basic functions for creating or modifying XStringViews objects
ByPos_MIndex-class | MIndex objects
B_WCP | Weighted Clustered Positions (WCP) objects
B_WCP-class | Weighted Clustered Positions (WCP) objects

## -- C --

cDNA | DNA/RNA transcription and translation
CharacterToFASTArecords | Read/write an XStringSet or XStringViews object from/to a file
chartr,ANY,ANY,MaskedXString-method | Translating letters of a sequence
chartr,ANY,ANY,XString-method | Translating letters of a sequence
chartr,ANY,ANY,XStringSet-method | Translating letters of a sequence
chartr,ANY,ANY,XStringViews-method | Translating letters of a sequence
class:AAKeySortedData | Data Dictionaries with XString-based Keys
class:AAKeySortedDataList | List of Data Dictionaries with XString-based Keys
class:AAString | AAString objects
class:AAStringSet | XStringSet objects
class:AAStringSetList | XStringSetList objects
class:AA_WCP | Weighted Clustered Positions (WCP) objects
class:ACtree | PDict objects
class:ACtree2 | PDict objects
class:AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
class:AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
class:BKeySortedData | Data Dictionaries with XString-based Keys
class:BKeySortedDataList | List of Data Dictionaries with XString-based Keys
class:BOC2_SubjectString | BOC\_SubjectString and BOC2\_SubjectString objects
class:BOC_SubjectString | BOC\_SubjectString and BOC2\_SubjectString objects
class:BString | BString objects
class:BStringSet | XStringSet objects
class:BStringSetList | XStringSetList objects
class:ByPos_MIndex | MIndex objects
class:B_WCP | Weighted Clustered Positions (WCP) objects
class:DNAKeySortedData | Data Dictionaries with XString-based Keys
class:DNAKeySortedDataList | List of Data Dictionaries with XString-based Keys
class:DNAString | DNAString objects
class:DNAStringSet | XStringSet objects
class:DNAStringSetList | XStringSetList objects
class:DNA_WCP | Weighted Clustered Positions (WCP) objects
class:Expanded_TB_PDict | PDict objects
class:InDel | InDel objects
class:MaskedAAString | MaskedXString objects
class:MaskedBString | MaskedXString objects
class:MaskedDNAString | MaskedXString objects
class:MaskedRNAString | MaskedXString objects
class:MaskedXString | MaskedXString objects
class:MIndex | MIndex objects
class:MTB_PDict | PDict objects
class:PairwiseAlignedFixedSubject | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PairwiseAlignedFixedSubjectSummary | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PairwiseAlignedXStringSet | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PDict | PDict objects
class:PDict3Parts | PDict objects
class:PhredQuality | PhredQuality and SolexaQuality objects
class:PreprocessedTB | PDict objects
class:QualityAlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
class:QualityScaledAAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledBStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledRNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:RNAKeySortedData | Data Dictionaries with XString-based Keys
class:RNAKeySortedDataList | List of Data Dictionaries with XString-based Keys
class:RNAString | RNAString objects
class:RNAStringSet | XStringSet objects
class:RNAStringSetList | XStringSetList objects
class:RNA_WCP | Weighted Clustered Positions (WCP) objects
class:SolexaQuality | PhredQuality and SolexaQuality objects
class:TB_PDict | PDict objects
class:Twobit | PDict objects
class:WCP | Weighted Clustered Positions (WCP) objects
class:XKeySortedData | Data Dictionaries with XString-based Keys
class:XKeySortedDataList | List of Data Dictionaries with XString-based Keys
class:XString | BString objects
class:XStringPartialMatches | XStringPartialMatches objects
class:XStringQuality | PhredQuality and SolexaQuality objects
class:XStringSet | XStringSet objects
class:XStringSetList | XStringSetList objects
class:XStringViews | The XStringViews class
codons | DNA/RNA transcription and translation
codons,DNAString-method | DNA/RNA transcription and translation
codons,MaskedDNAString-method | DNA/RNA transcription and translation
codons,MaskedRNAString-method | DNA/RNA transcription and translation
codons,RNAString-method | DNA/RNA transcription and translation
coerce,AAString,MaskedAAString-method | MaskedXString objects
coerce,BString,MaskedBString-method | MaskedXString objects
coerce,BString,PhredQuality-method | PhredQuality and SolexaQuality objects
coerce,BString,SolexaQuality-method | PhredQuality and SolexaQuality objects
coerce,BStringSet,PhredQuality-method | PhredQuality and SolexaQuality objects
coerce,BStringSet,SolexaQuality-method | PhredQuality and SolexaQuality objects
coerce,character,AAString-method | BString objects
coerce,character,AAStringSet-method | XStringSet objects
coerce,character,BString-method | BString objects
coerce,character,BStringSet-method | XStringSet objects
coerce,character,DNAString-method | BString objects
coerce,character,DNAStringSet-method | XStringSet objects
coerce,character,PhredQuality-method | PhredQuality and SolexaQuality objects
coerce,character,RNAString-method | BString objects
coerce,character,RNAStringSet-method | XStringSet objects
coerce,character,SolexaQuality-method | PhredQuality and SolexaQuality objects
coerce,character,XString-method | BString objects
coerce,character,XStringSet-method | XStringSet objects
coerce,DNAString,MaskedDNAString-method | MaskedXString objects
coerce,integer,PhredQuality-method | PhredQuality and SolexaQuality objects
coerce,integer,SolexaQuality-method | PhredQuality and SolexaQuality objects
coerce,MaskedAAString,AAString-method | MaskedXString objects
coerce,MaskedBString,BString-method | MaskedXString objects
coerce,MaskedDNAString,DNAString-method | MaskedXString objects
coerce,MaskedRNAString,RNAString-method | MaskedXString objects
coerce,MaskedXString,MaskCollection-method | MaskedXString objects
coerce,MaskedXString,MaskedAAString-method | MaskedXString objects
coerce,MaskedXString,MaskedBString-method | MaskedXString objects
coerce,MaskedXString,MaskedDNAString-method | MaskedXString objects
coerce,MaskedXString,MaskedRNAString-method | MaskedXString objects
coerce,MaskedXString,NormalIRanges-method | MaskedXString objects
coerce,MaskedXString,Views-method | MaskedXString objects
coerce,MaskedXString,XStringViews-method | MaskedXString objects
coerce,MIndex,CompressedIRangesList-method | MIndex objects
coerce,numeric,PhredQuality-method | PhredQuality and SolexaQuality objects
coerce,numeric,SolexaQuality-method | PhredQuality and SolexaQuality objects
coerce,PhredQuality,integer-method | PhredQuality and SolexaQuality objects
coerce,PhredQuality,numeric-method | PhredQuality and SolexaQuality objects
coerce,RNAString,MaskedRNAString-method | MaskedXString objects
coerce,SolexaQuality,integer-method | PhredQuality and SolexaQuality objects
coerce,SolexaQuality,numeric-method | PhredQuality and SolexaQuality objects
coerce,XString,AAString-method | BString objects
coerce,XString,AAStringSet-method | XStringSet objects
coerce,XString,BString-method | BString objects
coerce,XString,BStringSet-method | XStringSet objects
coerce,XString,DNAString-method | BString objects
coerce,XString,DNAStringSet-method | XStringSet objects
coerce,XString,RNAString-method | BString objects
coerce,XString,RNAStringSet-method | XStringSet objects
coerce,XString,XStringSet-method | XStringSet objects
coerce,XStringSet,AAStringSet-method | XStringSet objects
coerce,XStringSet,BStringSet-method | XStringSet objects
coerce,XStringSet,DNAStringSet-method | XStringSet objects
coerce,XStringSet,RNAStringSet-method | XStringSet objects
coerce,XStringViews,AAStringSet-method | The XStringViews class
coerce,XStringViews,BStringSet-method | The XStringViews class
coerce,XStringViews,DNAStringSet-method | The XStringViews class
coerce,XStringViews,RNAStringSet-method | The XStringViews class
coerce,XStringViews,XStringSet-method | The XStringViews class
collapse,MaskedXString-method | MaskedXString objects
compact | XStringSet objects
compact,XStringSet-method | XStringSet objects
compareStrings | Utility functions related to sequence alignment
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method | Utility functions related to sequence alignment
compareStrings,character,character-method | Utility functions related to sequence alignment
compareStrings,PairwiseAlignedXStringSet,missing-method | Utility functions related to sequence alignment
compareStrings,XString,XString-method | Utility functions related to sequence alignment
compareStrings,XStringSet,XStringSet-method | Utility functions related to sequence alignment
complement | Sequence reversing and complementing
complement,DNAString-method | Sequence reversing and complementing
complement,DNAStringSet-method | Sequence reversing and complementing
complement,MaskedDNAString-method | Sequence reversing and complementing
complement,MaskedRNAString-method | Sequence reversing and complementing
complement,RNAString-method | Sequence reversing and complementing
complement,RNAStringSet-method | Sequence reversing and complementing
complement,XStringViews-method | Sequence reversing and complementing
complementedPalindromeArmLength | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,DNAString-method | Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
complementSeq | Complementary sequence.
consensusMatrix | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix,character-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix,list-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix,matrix-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix,PairwiseAlignedFixedSubject-method | Utility functions related to sequence alignment
consensusMatrix,XStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix,XStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,ANY-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,BStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,BStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,DNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,DNAStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,matrix-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,RNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString,RNAStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consmat | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consmat,ANY-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
countbases | Obtain the ATCG content of a gene
countIndex | MIndex objects
countIndex,ByPos_MIndex-method | MIndex objects
countIndex,MIndex-method | MIndex objects
countPattern | String searching functions
countPattern,BOC2_SubjectString-method | BOC\_SubjectString and BOC2\_SubjectString objects
countPattern,character-method | String searching functions
countPattern,MaskedXString-method | String searching functions
countPattern,XString-method | String searching functions
countPattern,XStringSet-method | String searching functions
countPattern,XStringViews-method | String searching functions
countPDict | Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,MaskedXString-method | Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XString-method | Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XStringSet-method | Searching a sequence for patterns stored in a preprocessed dictionary
countPDict,XStringViews-method | Searching a sequence for patterns stored in a preprocessed dictionary
countPWM | PWM creating, matching, and related utilities
countPWM,character-method | PWM creating, matching, and related utilities
countPWM,DNAString-method | PWM creating, matching, and related utilities
countPWM,MaskedDNAString-method | PWM creating, matching, and related utilities
countPWM,XStringViews-method | PWM creating, matching, and related utilities
countWCP | A simple WCP matching function and related utilities
countWCP,character-method | A simple WCP matching function and related utilities
countWCP,MaskedXString-method | A simple WCP matching function and related utilities
countWCP,XString-method | A simple WCP matching function and related utilities
countWCP,XStringViews-method | A simple WCP matching function and related utilities
coverage,AlignedXStringSet0-method | Utility functions related to sequence alignment
coverage,MaskedXString-method | Utility functions operating on the matches returned by a high-level matching function
coverage,MIndex-method | Utility functions operating on the matches returned by a high-level matching function
coverage,PairwiseAlignedFixedSubject-method | Utility functions related to sequence alignment
coverage,PairwiseAlignedFixedSubjectSummary-method | Utility functions related to sequence alignment

## -- D --

dataKey | Data Dictionaries with XString-based Keys
dataKey,XKeySortedData-method | Data Dictionaries with XString-based Keys
dataTable | Data Dictionaries with XString-based Keys
dataTable,XKeySortedData-method | Data Dictionaries with XString-based Keys
deletion | InDel objects
deletion,InDel-method | InDel objects
deletion,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
dim,XKeySortedData-method | Data Dictionaries with XString-based Keys
dimnames,XKeySortedData-method | Data Dictionaries with XString-based Keys
dinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
dinucleotideFrequencyTest | Pearson's chi-squared Test and G-tests for String Position Dependence
dinucleotideFrequencyTest,DNAStringSet-method | Pearson's chi-squared Test and G-tests for String Position Dependence
dinucleotideFrequencyTest,RNAStringSet-method | Pearson's chi-squared Test and G-tests for String Position Dependence
dna2rna | DNA/RNA transcription and translation
DNAKeySortedData | Data Dictionaries with XString-based Keys
DNAKeySortedData-class | Data Dictionaries with XString-based Keys
DNAKeySortedDataList | List of Data Dictionaries with XString-based Keys
DNAKeySortedDataList-class | List of Data Dictionaries with XString-based Keys
DNAString | DNAString objects
DNAString-class | DNAString objects
DNAStringSet | XStringSet objects
DNAStringSet-class | XStringSet objects
DNAStringSetList | XStringSetList objects
DNAStringSetList-class | XStringSetList objects
DNA_ALPHABET | DNAString objects
DNA_BASES | DNAString objects
DNA_WCP | Weighted Clustered Positions (WCP) objects
DNA_WCP-class | Weighted Clustered Positions (WCP) objects
duplicated,PDict-method | PDict objects
duplicated,PreprocessedTB-method | PDict objects
duplicated,XStringSet-method | XStringSet objects

## -- E --

end,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
endIndex | MIndex objects
endIndex,ByPos_MIndex-method | MIndex objects
errorSubstitutionMatrices | Scoring matrices
Expanded_TB_PDict | PDict objects
Expanded_TB_PDict-class | PDict objects
extractAllMatches | Searching a sequence for patterns stored in a preprocessed dictionary
extractTranscripts | Extract a set of transcripts

## -- F --

fasta.info | Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToBStringViews | Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToCharacter | Read/write an XStringSet or XStringViews object from/to a file
FASTArecordsToXStringViews | Read/write an XStringSet or XStringViews object from/to a file
fastq.geometry | Read/write an XStringSet or XStringViews object from/to a file
findComplementedPalindromes | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,DNAString-method | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,MaskedXString-method | Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes,XStringViews-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes | Searching a sequence for palindromes or complemented palindromes
findPalindromes,MaskedXString-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes,XString-method | Searching a sequence for palindromes or complemented palindromes
findPalindromes,XStringViews-method | Searching a sequence for palindromes or complemented palindromes

## -- G --

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

## -- H --

hasLetterAt | Low-level matching functions
hasOnlyBaseLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,DNAString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,DNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,MaskedXString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,RNAString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,RNAStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters,XStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
head,PDict3Parts-method | PDict objects
head,TB_PDict-method | PDict objects
HNF4alpha | Known HNF4alpha binding sequences

## -- I --

InDel | InDel objects
indel | AlignedXStringSet and QualityAlignedXStringSet objects
indel,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
indel,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
InDel-class | InDel objects
initialize,ACtree-method | PDict objects
initialize,ACtree2-method | PDict objects
initialize,BOC2_SubjectString-method | BOC\_SubjectString and BOC2\_SubjectString objects
initialize,BOC_SubjectString-method | BOC\_SubjectString and BOC2\_SubjectString objects
initialize,PreprocessedTB-method | PDict objects
initialize,Twobit-method | PDict objects
injectHardMask | Injecting a hard mask in a sequence
injectHardMask,MaskedXString-method | Injecting a hard mask in a sequence
injectHardMask,XStringViews-method | Injecting a hard mask in a sequence
insertion | InDel objects
insertion,InDel-method | InDel objects
insertion,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
intersect,XStringSet,XStringSet-method | XStringSet objects
is.unsorted,XStringSet-method | XStringSet objects
isMatching | Low-level matching functions
isMatchingAt | Low-level matching functions
isMatchingEndingAt | Low-level matching functions
isMatchingEndingAt,character-method | Low-level matching functions
isMatchingEndingAt,XString-method | Low-level matching functions
isMatchingEndingAt,XStringSet-method | Low-level matching functions
isMatchingStartingAt | Low-level matching functions
isMatchingStartingAt,character-method | Low-level matching functions
isMatchingStartingAt,XString-method | Low-level matching functions
isMatchingStartingAt,XStringSet-method | Low-level matching functions
IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet

## -- L --

lcprefix | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcprefix,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,character,XString-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,character-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix,XString,XString-method | Longest Common Prefix/Suffix/Substring searching functions
length,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
length,MaskedXString-method | MaskedXString objects
length,MIndex-method | MIndex objects
length,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
length,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
length,PDict-method | PDict objects
length,PDict3Parts-method | PDict objects
length,PreprocessedTB-method | PDict objects
length,XKeySortedData-method | Data Dictionaries with XString-based Keys
length,XStringSetList-method | XStringSetList objects
letter | Subsetting a string
letter,character-method | Subsetting a string
letter,MaskedXString-method | Subsetting a string
letter,XString-method | Subsetting a string
letter,XStringViews-method | Subsetting a string
letterFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
letterFrequencyInSlidingView | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
letterFrequencyInSlidingView,XString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
longestConsecutive | Obtain the length of the longest substring containing only 'letter'
lowlevel-matching | Low-level matching functions

## -- M --

mask | Masking by content (or by position)
MaskedAAString | MaskedXString objects
MaskedAAString-class | MaskedXString objects
MaskedBString | MaskedXString objects
MaskedBString-class | MaskedXString objects
MaskedDNAString | MaskedXString objects
MaskedDNAString-class | MaskedXString objects
maskedratio,MaskedXString-method | MaskedXString objects
MaskedRNAString | MaskedXString objects
MaskedRNAString-class | MaskedXString objects
maskedwidth,MaskedXString-method | MaskedXString objects
MaskedXString | MaskedXString objects
MaskedXString-class | MaskedXString objects
maskMotif | Masking by content (or by position)
maskMotif,MaskedXString,character-method | Masking by content (or by position)
maskMotif,MaskedXString,XString-method | Masking by content (or by position)
maskMotif,XString,ANY-method | Masking by content (or by position)
masks | MaskedXString objects
masks,MaskedXString-method | MaskedXString objects
masks,XString-method | MaskedXString objects
masks<- | MaskedXString objects
masks<-,MaskedXString,MaskCollection-method | MaskedXString objects
masks<-,MaskedXString,NULL-method | MaskedXString objects
masks<-,XString,ANY-method | MaskedXString objects
masks<-,XString,NULL-method | MaskedXString objects
match,character,XStringSet-method | XStringSet objects
match,XString,XStringSet-method | XStringSet objects
match,XStringSet,XStringSet-method | XStringSet objects
match-utils | Utility functions operating on the matches returned by a high-level matching function
matchDNAPattern | String searching functions
matchLRPatterns | Find paired matches in a sequence
matchLRPatterns,MaskedXString-method | Find paired matches in a sequence
matchLRPatterns,XString-method | Find paired matches in a sequence
matchLRPatterns,XStringViews-method | Find paired matches in a sequence
matchPattern | String searching functions
matchPattern,BOC2_SubjectString-method | BOC\_SubjectString and BOC2\_SubjectString objects
matchPattern,BOC_SubjectString-method | BOC\_SubjectString and BOC2\_SubjectString objects
matchPattern,character-method | String searching functions
matchPattern,MaskedXString-method | String searching functions
matchPattern,XString-method | String searching functions
matchPattern,XStringSet-method | String searching functions
matchPattern,XStringViews-method | String searching functions
matchPDict | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,MaskedXString-method | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XString-method | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XStringSet-method | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict,XStringViews-method | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict-exact | Searching a sequence for patterns stored in a preprocessed dictionary
matchPDict-inexact | Inexact matching with matchPDict()/countPDict()/whichPDict()
matchProbePair | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,DNAString-method | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,MaskedDNAString-method | Find "theoretical amplicons" mapped to a probe pair
matchProbePair,XStringViews-method | Find "theoretical amplicons" mapped to a probe pair
matchprobes | A function to match a query sequence to the sequences of a set of probes.
matchPWM | PWM creating, matching, and related utilities
matchPWM,character-method | PWM creating, matching, and related utilities
matchPWM,DNAString-method | PWM creating, matching, and related utilities
matchPWM,MaskedDNAString-method | PWM creating, matching, and related utilities
matchPWM,XStringViews-method | PWM creating, matching, and related utilities
matchWCP | A simple WCP matching function and related utilities
matchWCP,character-method | A simple WCP matching function and related utilities
matchWCP,MaskedXString-method | A simple WCP matching function and related utilities
matchWCP,XString-method | A simple WCP matching function and related utilities
matchWCP,XStringViews-method | A simple WCP matching function and related utilities
maxScore | PWM creating, matching, and related utilities
maxScore,ANY-method | PWM creating, matching, and related utilities
maxWeights | PWM creating, matching, and related utilities
maxWeights,matrix-method | PWM creating, matching, and related utilities
maxWeights,WCP-method | Weighted Clustered Positions (WCP) objects
mergeIUPACLetters | The IUPAC Extended Genetic Alphabet
MIndex | MIndex objects
MIndex-class | MIndex objects
minScore | PWM creating, matching, and related utilities
minScore,ANY-method | PWM creating, matching, and related utilities
minWeights | PWM creating, matching, and related utilities
minWeights,matrix-method | PWM creating, matching, and related utilities
misc | Some miscellaneous stuff
mismatch | Utility functions operating on the matches returned by a high-level matching function
mismatch,AlignedXStringSet0,missing-method | Utility functions related to sequence alignment
mismatch,ANY,XStringViews-method | Utility functions operating on the matches returned by a high-level matching function
mismatchSummary | Utility functions related to sequence alignment
mismatchSummary,AlignedXStringSet0-method | Utility functions related to sequence alignment
mismatchSummary,PairwiseAlignedFixedSubject-method | Utility functions related to sequence alignment
mismatchSummary,PairwiseAlignedFixedSubjectSummary-method | Utility functions related to sequence alignment
mismatchSummary,QualityAlignedXStringSet-method | Utility functions related to sequence alignment
mismatchTable | Utility functions related to sequence alignment
mismatchTable,AlignedXStringSet0-method | Utility functions related to sequence alignment
mismatchTable,PairwiseAlignedXStringSet-method | Utility functions related to sequence alignment
mismatchTable,QualityAlignedXStringSet-method | Utility functions related to sequence alignment
mkAllStrings | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
MTB_PDict | PDict objects
MTB_PDict-class | PDict objects

## -- N --

N50 | Some miscellaneous stuff
names,MIndex-method | MIndex objects
names,PDict-method | PDict objects
names,XStringSetList-method | XStringSetList objects
names<-,MIndex-method | MIndex objects
names<-,PDict-method | PDict objects
names<-,XStringSetList-method | XStringSetList objects
narrow,character-method | XStringSet objects
narrow,QualityScaledXStringSet-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
nchar,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
nchar,MaskedXString-method | MaskedXString objects
nchar,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
nchar,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
nchar,XString-method | BString objects
nchar,XStringSet-method | XStringSet objects
nchar,XStringViews-method | The XStringViews class
nedit | Utility functions related to sequence alignment
nedit,PairwiseAlignedFixedSubjectSummary-method | Utility functions related to sequence alignment
nedit,PairwiseAlignedXStringSet-method | Utility functions related to sequence alignment
neditAt | Low-level matching functions
neditEndingAt | Low-level matching functions
neditEndingAt,character-method | Low-level matching functions
neditEndingAt,XString-method | Low-level matching functions
neditEndingAt,XStringSet-method | Low-level matching functions
neditStartingAt | Low-level matching functions
neditStartingAt,character-method | Low-level matching functions
neditStartingAt,XString-method | Low-level matching functions
neditStartingAt,XStringSet-method | Low-level matching functions
needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,character-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,character,XString-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,character-method | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS,XString,XString-method | (Deprecated) Needleman-Wunsch Global Alignment
nindel | AlignedXStringSet and QualityAlignedXStringSet objects
nindel,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
nindel,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
nindel,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
nmatch | Utility functions operating on the matches returned by a high-level matching function
nmatch,ANY,XStringViews-method | Utility functions operating on the matches returned by a high-level matching function
nmatch,PairwiseAlignedFixedSubjectSummary,missing-method | Utility functions related to sequence alignment
nmatch,PairwiseAlignedXStringSet,missing-method | Utility functions related to sequence alignment
nmismatch | Utility functions operating on the matches returned by a high-level matching function
nmismatch,AlignedXStringSet0,missing-method | Utility functions related to sequence alignment
nmismatch,ANY,XStringViews-method | Utility functions operating on the matches returned by a high-level matching function
nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method | Utility functions related to sequence alignment
nmismatch,PairwiseAlignedXStringSet,missing-method | Utility functions related to sequence alignment
nmismatchEndingAt | Low-level matching functions
nmismatchStartingAt | Low-level matching functions
nnodes | PDict objects
nnodes,ACtree2-method | PDict objects
nucleotideFrequencyAt | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
nucleotideFrequencyAt,XStringSet-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
nucleotideFrequencyAt,XStringViews-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
nucleotideSubstitutionMatrix | Scoring matrices

## -- O --

oligonucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideFrequency,MaskedXString-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideFrequency,XString-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideFrequency,XStringSet-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideFrequency,XStringViews-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideTransitions | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
order,XStringSet-method | XStringSet objects

## -- P --

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

## -- Q --

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

## -- R --

rank,XStringSet-method | XStringSet objects
read.AAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.BStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.BStringViews | Read/write an XStringSet or XStringViews object from/to a file
read.DNAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.RNAStringSet | Read/write an XStringSet or XStringViews object from/to a file
read.XStringViews | Read/write an XStringSet or XStringViews object from/to a file
readFASTA | Functions to read/write FASTA formatted files
rep,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
rep,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
rep,XStringSet-method | XStringSet objects
replaceLetterAt | Replacing letters in a sequence (or set of sequences) at some specified locations
replaceLetterAt,DNAString-method | Replacing letters in a sequence (or set of sequences) at some specified locations
replaceLetterAt,DNAStringSet-method | Replacing letters in a sequence (or set of sequences) at some specified locations
replaceLetterAtLoc | Replacing letters in a sequence (or set of sequences) at some specified locations
revcompDNA | Reverse Sequence
revcompRNA | Reverse Sequence
reverse,character-method | Sequence reversing and complementing
reverse,MaskedXString-method | Sequence reversing and complementing
reverse,XString-method | Sequence reversing and complementing
reverse,XStringSet-method | Sequence reversing and complementing
reverse,XStringViews-method | Sequence reversing and complementing
reverseComplement | Sequence reversing and complementing
reverseComplement,DNAString-method | Sequence reversing and complementing
reverseComplement,DNAStringSet-method | Sequence reversing and complementing
reverseComplement,MaskedDNAString-method | Sequence reversing and complementing
reverseComplement,MaskedRNAString-method | Sequence reversing and complementing
reverseComplement,matrix-method | PWM creating, matching, and related utilities
reverseComplement,RNAString-method | Sequence reversing and complementing
reverseComplement,RNAStringSet-method | Sequence reversing and complementing
reverseComplement,XStringViews-method | Sequence reversing and complementing
reverseSeq | Reverse Sequence
rna2dna | DNA/RNA transcription and translation
RNAKeySortedData | Data Dictionaries with XString-based Keys
RNAKeySortedData-class | Data Dictionaries with XString-based Keys
RNAKeySortedDataList | List of Data Dictionaries with XString-based Keys
RNAKeySortedDataList-class | List of Data Dictionaries with XString-based Keys
RNAString | RNAString objects
RNAString-class | RNAString objects
RNAStringSet | XStringSet objects
RNAStringSet-class | XStringSet objects
RNAStringSetList | XStringSetList objects
RNAStringSetList-class | XStringSetList objects
RNA_ALPHABET | RNAString objects
RNA_BASES | RNAString objects
RNA_GENETIC_CODE | The Standard Genetic Code
RNA_WCP | Weighted Clustered Positions (WCP) objects
RNA_WCP-class | Weighted Clustered Positions (WCP) objects

## -- S --

save.XStringSet | Read/write an XStringSet or XStringViews object from/to a file
score,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
score,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
setdiff,XStringSet,XStringSet-method | XStringSet objects
setequal,XStringSet,XStringSet-method | XStringSet objects
show,ACtree-method | PDict objects
show,ACtree2-method | PDict objects
show,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
show,ByPos_MIndex-method | MIndex objects
show,MaskedXString-method | MaskedXString objects
show,MTB_PDict-method | PDict objects
show,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
show,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
show,QualityScaledXStringSet-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
show,TB_PDict-method | PDict objects
show,Twobit-method | PDict objects
show,WCP-method | Weighted Clustered Positions (WCP) objects
show,XString-method | BString objects
show,XStringPartialMatches-method | XStringPartialMatches objects
show,XStringSet-method | XStringSet objects
show,XStringSetList-method | XStringSetList objects
show,XStringViews-method | The XStringViews class
SolexaQuality | PhredQuality and SolexaQuality objects
SolexaQuality-class | PhredQuality and SolexaQuality objects
sort,XStringSet-method | XStringSet objects
srPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads
start,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
startIndex | MIndex objects
startIndex,ByPos_MIndex-method | MIndex objects
stringDist | String Distance/Alignment Score Matrix
stringDist,character-method | String Distance/Alignment Score Matrix
stringDist,QualityScaledXStringSet-method | String Distance/Alignment Score Matrix
stringDist,XStringSet-method | String Distance/Alignment Score Matrix
strrev | Sequence reversing and complementing
subBString | Fast substring extraction
subject,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
subpatterns | XStringPartialMatches objects
subpatterns,XStringPartialMatches-method | XStringPartialMatches objects
subseq,character-method | XStringSet objects
subseq,MaskedXString-method | MaskedXString objects
subseq<-,character-method | XStringSet objects
subseq<-,XStringSet-method | XStringSet objects
substitution.matrices | Scoring matrices
substr,MaskedXString-method | Fast substring extraction
substr,XString-method | Fast substring extraction
substring,MaskedXString-method | Fast substring extraction
substring,XString-method | Fast substring extraction
subXString | Fast substring extraction
summary,PairwiseAlignedFixedSubject-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects

## -- T --

tail,PDict3Parts-method | PDict objects
tail,TB_PDict-method | PDict objects
tb | PDict objects
tb,PDict3Parts-method | PDict objects
tb,PreprocessedTB-method | PDict objects
tb,TB_PDict-method | PDict objects
tb.width | PDict objects
tb.width,PDict3Parts-method | PDict objects
tb.width,PreprocessedTB-method | PDict objects
tb.width,TB_PDict-method | PDict objects
TB_PDict | PDict objects
TB_PDict-class | PDict objects
threebands,character-method | XStringSet objects
toComplex | Turning a DNA sequence into a vector of complex numbers
toComplex,DNAString-method | Turning a DNA sequence into a vector of complex numbers
toString,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
toString,MaskedXString-method | MaskedXString objects
toString,PairwiseAlignedFixedSubject-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
toString,XString-method | BString objects
toString,XStringSet-method | XStringSet objects
toString,XStringViews-method | The XStringViews class
transcribe | DNA/RNA transcription and translation
transcriptLocs2refLocs | Extract a set of transcripts
transcriptWidths | Extract a set of transcripts
translate | DNA/RNA transcription and translation
translate,DNAString-method | DNA/RNA transcription and translation
translate,DNAStringSet-method | DNA/RNA transcription and translation
translate,MaskedDNAString-method | DNA/RNA transcription and translation
translate,MaskedRNAString-method | DNA/RNA transcription and translation
translate,RNAString-method | DNA/RNA transcription and translation
translate,RNAStringSet-method | DNA/RNA transcription and translation
trimLRPatterns | Trim Flanking Patterns from Sequences
trimLRPatterns,character-method | Trim Flanking Patterns from Sequences
trimLRPatterns,XString-method | Trim Flanking Patterns from Sequences
trimLRPatterns,XStringSet-method | Trim Flanking Patterns from Sequences
trinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
Twobit | PDict objects
Twobit-class | PDict objects
type | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
type,PairwiseAlignedFixedSubjectSummary-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
type,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects

## -- U --

unaligned | AlignedXStringSet and QualityAlignedXStringSet objects
unaligned,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
union,XStringSet,XStringSet-method | XStringSet objects
unique,XStringSet-method | XStringSet objects
uniqueLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
uniqueLetters,MaskedXString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
uniqueLetters,XString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
uniqueLetters,XStringSet-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
uniqueLetters,XStringViews-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
unitScale | PWM creating, matching, and related utilities
unlist,MIndex-method | MIndex objects
unlist,XStringSet-method | XStringSet objects
unlist,XStringSetList-method | XStringSetList objects
unmasked | MaskedXString objects
unmasked,MaskedXString-method | MaskedXString objects
updateObject,XString-method | BString objects
updateObject,XStringSet-method | XStringSet objects

## -- V --

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

## -- W --

WCP | Weighted Clustered Positions (WCP) objects
WCP-class | Weighted Clustered Positions (WCP) objects
WCPscoreStartingAt | A simple WCP matching function and related utilities
which.isMatchingAt | Low-level matching functions
which.isMatchingEndingAt | Low-level matching functions
which.isMatchingEndingAt,character-method | Low-level matching functions
which.isMatchingEndingAt,XString-method | Low-level matching functions
which.isMatchingEndingAt,XStringSet-method | Low-level matching functions
which.isMatchingStartingAt | Low-level matching functions
which.isMatchingStartingAt,character-method | Low-level matching functions
which.isMatchingStartingAt,XString-method | Low-level matching functions
which.isMatchingStartingAt,XStringSet-method | Low-level matching functions
whichPDict | Searching a sequence for patterns stored in a preprocessed dictionary
whichPDict,XString-method | Searching a sequence for patterns stored in a preprocessed dictionary
width,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
width,character-method | XStringSet objects
width,PDict-method | PDict objects
width,PDict3Parts-method | PDict objects
width,PreprocessedTB-method | PDict objects
width0 | MIndex objects
width0,MIndex-method | MIndex objects
write.BStringViews | Read/write an XStringSet or XStringViews object from/to a file
write.XStringSet | Read/write an XStringSet or XStringViews object from/to a file
write.XStringViews | Read/write an XStringSet or XStringViews object from/to a file
writeFASTA | Functions to read/write FASTA formatted files
wtPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads

## -- X --

XKeySortedData | Data Dictionaries with XString-based Keys
XKeySortedData-class | Data Dictionaries with XString-based Keys
XKeySortedDataList | List of Data Dictionaries with XString-based Keys
XKeySortedDataList-class | List of Data Dictionaries with XString-based Keys
xsbasetype,AAString-method | BString objects
xsbasetype,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
xsbasetype,BString-method | BString objects
xsbasetype,DNAString-method | BString objects
xsbasetype,MaskedXString-method | MaskedXString objects
xsbasetype,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
xsbasetype,RNAString-method | BString objects
xsbasetype,WCP-method | Weighted Clustered Positions (WCP) objects
xsbasetype,XKeySortedData-method | Data Dictionaries with XString-based Keys
xsbasetype,XKeySortedDataList-method | List of Data Dictionaries with XString-based Keys
xsbasetype,XStringSet-method | XStringSet objects
xsbasetype,XStringSetList-method | XStringSetList objects
xsbasetype,XStringViews-method | The XStringViews class
xsbasetype<-,MaskedXString-method | MaskedXString objects
xsbasetype<-,XString-method | BString objects
xsbasetype<-,XStringSet-method | XStringSet objects
xsbasetype<-,XStringSetList-method | XStringSetList objects
xsbasetype<-,XStringViews-method | The XStringViews class
xscat | Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
XString | BString objects
XString-class | BString objects
XStringPartialMatches-class | XStringPartialMatches objects
XStringQuality | PhredQuality and SolexaQuality objects
XStringQuality-class | PhredQuality and SolexaQuality objects
XStringSet | XStringSet objects
XStringSet-class | XStringSet objects
XStringSetList | XStringSetList objects
XStringSetList-class | XStringSetList objects
XStringSetToFASTArecords | Read/write an XStringSet or XStringViews object from/to a file
XStringViews | Basic functions for creating or modifying XStringViews objects
XStringViews,ANY-method | Basic functions for creating or modifying XStringViews objects
XStringViews,XString-method | Basic functions for creating or modifying XStringViews objects
XStringViews,XStringViews-method | Basic functions for creating or modifying XStringViews objects
XStringViews-class | The XStringViews class
XStringViews-constructors | Basic functions for creating or modifying XStringViews objects

## -- Y --

yeastSEQCHR1 | An annotation data file for CHR1 in the yeastSEQ package

## -- misc --

[,ACtree-method | PDict objects
[,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
[,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
[,QualityScaledXStringSet-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
[,XKeySortedData-method | Data Dictionaries with XString-based Keys
[,XStringPartialMatches-method | XStringPartialMatches objects
[,XStringSet-method | XStringSet objects
[<-,AlignedXStringSet0-method | AlignedXStringSet and QualityAlignedXStringSet objects
[<-,PairwiseAlignedXStringSet-method | PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
[[,ByPos_MIndex-method | MIndex objects
[[,PDict-method | PDict objects
[[,XKeySortedData-method | Data Dictionaries with XString-based Keys
[[,XStringSetList-method | XStringSetList objects
[[<-,XStringSetList-method | XStringSetList objects