String objects representing biological sequences, and matching algorithms

[Package List] [Top]

Documentation for package ‘Biostrings’ version 2.14.12

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

A B C D E F G H I L M N O P Q R S T U V W X Y misc

-- --

!=,BString,character-method BString objects
!=,character,BString-method BString objects
!=,character,XStringViews-method The XStringViews class
!=,XString,XString-method BString objects
!=,XString,XStringViews-method The XStringViews class
!=,XStringViews,character-method The XStringViews class
!=,XStringViews,XString-method The XStringViews class
!=,XStringViews,XStringViews-method The XStringViews class
%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