Entry: AAString-class
Aliases: class:AAString AAString-class AA_ALPHABET AAString
Keywords: methods classes
Description: AAString objects
URL: ../../../library/Biostrings/html/AAString-class.html

Entry: AMINO_ACID_CODE
Aliases: AMINO_ACID_CODE
Keywords: utilities data
Description: The Single-Letter Amino Acid Code
URL: ../../../library/Biostrings/html/AMINO_ACID_CODE.html

Entry: AlignedXStringSet-class
Aliases: class:AlignedXStringSet0 AlignedXStringSet0-class AlignedXStringSet0 class:AlignedXStringSet AlignedXStringSet-class AlignedXStringSet class:QualityAlignedXStringSet QualityAlignedXStringSet-class QualityAlignedXStringSet unaligned unaligned,AlignedXStringSet0-method aligned aligned,AlignedXStringSet0-method start,AlignedXStringSet0-method end,AlignedXStringSet0-method width,AlignedXStringSet0-method indel indel,AlignedXStringSet0-method nindel nindel,AlignedXStringSet0-method length,AlignedXStringSet0-method nchar,AlignedXStringSet0-method xsbasetype,AlignedXStringSet0-method show,AlignedXStringSet0-method as.character,AlignedXStringSet0-method toString,AlignedXStringSet0-method [,AlignedXStringSet0-method [<-,AlignedXStringSet0-method rep,AlignedXStringSet0-method
Keywords: methods classes
Description: AlignedXStringSet and QualityAlignedXStringSet objects
URL: ../../../library/Biostrings/html/AlignedXStringSet-class.html

Entry: BOC_SubjectString-class
Aliases: class:BOC_SubjectString BOC_SubjectString-class BOC_SubjectString class:BOC2_SubjectString BOC2_SubjectString-class BOC2_SubjectString initialize,BOC_SubjectString-method initialize,BOC2_SubjectString-method matchPattern,BOC_SubjectString-method matchPattern,BOC2_SubjectString-method countPattern,BOC2_SubjectString-method
Keywords: methods classes
Description: BOC\_SubjectString and BOC2\_SubjectString objects
URL: ../../../library/Biostrings/html/BOC_SubjectString-class.html

Entry: Biostrings internals
Aliases: class:Dups Dups-class Dups length,Dups-method duplicated,Dups-method show,Dups-method class:SparseList SparseList-class SparseList length,SparseList-method ls,SparseList-method as.list,SparseList-method [[,SparseList-method class:XStringCodec XStringCodec-class XStringCodec initialize,XStringCodec-method xsbasetype xsbasetype<-
Keywords: internal methods classes
Description: Biostrings internals
URL: ../../../library/Biostrings/html/Biostrings-internals.html

Entry: DNAString-class
Aliases: class:DNAString DNAString-class DNA_BASES DNA_ALPHABET DNAString
Keywords: methods classes
Description: DNAString objects
URL: ../../../library/Biostrings/html/DNAString-class.html

Entry: GENETIC_CODE
Aliases: GENETIC_CODE RNA_GENETIC_CODE
Keywords: utilities data
Description: The Standard Genetic Code
URL: ../../../library/Biostrings/html/GENETIC_CODE.html

Entry: IUPAC_CODE_MAP
Aliases: IUPAC_CODE_MAP mergeIUPACLetters
Keywords: utilities data
Description: The IUPAC Extended Genetic Alphabet
URL: ../../../library/Biostrings/html/IUPAC_CODE_MAP.html

Entry: InDel-class
Aliases: class:InDel InDel-class InDel insertion insertion,InDel-method deletion deletion,InDel-method
Keywords: methods classes
Description: InDel objects
URL: ../../../library/Biostrings/html/InDel-class.html

Entry: MIndex-class
Aliases: MIndex class:MIndex MIndex-class class:ByPos_MIndex ByPos_MIndex-class length,MIndex-method width,MIndex-method names,MIndex-method names<-,MIndex-method startIndex endIndex countIndex countIndex,MIndex-method unlist,MIndex-method show,ByPos_MIndex-method [[,ByPos_MIndex-method startIndex,ByPos_MIndex-method endIndex,ByPos_MIndex-method countIndex,ByPos_MIndex-method
Keywords: methods classes
Description: MIndex objects
URL: ../../../library/Biostrings/html/MIndex-class.html

Entry: MaskedXString-class
Aliases: class:MaskedXString MaskedXString-class MaskedXString class:MaskedBString MaskedBString-class MaskedBString class:MaskedDNAString MaskedDNAString-class MaskedDNAString class:MaskedRNAString MaskedRNAString-class MaskedRNAString class:MaskedAAString MaskedAAString-class MaskedAAString unmasked unmasked,MaskedXString-method masks masks,XString-method masks,MaskedXString-method length,MaskedXString-method maskedwidth,MaskedXString-method maskedratio,MaskedXString-method nchar,MaskedXString-method xsbasetype,MaskedXString-method xsbasetype<-,MaskedXString-method coerce,MaskedXString,MaskedBString-method coerce,MaskedXString,MaskedDNAString-method coerce,MaskedXString,MaskedRNAString-method coerce,MaskedXString,MaskedAAString-method coerce,BString,MaskedBString-method coerce,DNAString,MaskedDNAString-method coerce,RNAString,MaskedRNAString-method coerce,AAString,MaskedAAString-method coerce,MaskedBString,BString-method coerce,MaskedDNAString,DNAString-method coerce,MaskedRNAString,RNAString-method coerce,MaskedAAString,AAString-method coerce,MaskedXString,MaskCollection-method coerce,MaskedXString,NormalIRanges-method coerce,MaskedXString,XStringViews-method coerce,MaskedXString,Views-method reduce,MaskedXString-method gaps,MaskedXString-method subseq,MaskedXString-method as.character,MaskedXString-method toString,MaskedXString-method show,MaskedXString-method masks<- masks<-,MaskedXString,NULL-method masks<-,MaskedXString,MaskCollection-method masks<-,XString,NULL-method masks<-,XString,ANY-method Views,MaskedXString-method
Keywords: methods classes
Description: MaskedXString objects
URL: ../../../library/Biostrings/html/MaskedXString-class.html

Entry: PDict-class
Aliases: class:PreprocessedTB PreprocessedTB-class PreprocessedTB length,PreprocessedTB-method width,PreprocessedTB-method tb tb,PreprocessedTB-method tb.width tb.width,PreprocessedTB-method initialize,PreprocessedTB-method duplicated,PreprocessedTB-method class:Twobit Twobit-class Twobit show,Twobit-method initialize,Twobit-method class:ACtree ACtree-class ACtree show,ACtree-method [,ACtree-method as.matrix,ACtree-method initialize,ACtree-method class:ACtree2 ACtree2-class ACtree2 show,ACtree2-method initialize,ACtree2-method class:PDict3Parts PDict3Parts-class PDict3Parts length,PDict3Parts-method width,PDict3Parts-method head,PDict3Parts-method tb,PDict3Parts-method tb.width,PDict3Parts-method tail,PDict3Parts-method class:PDict PDict-class length,PDict-method width,PDict-method names,PDict-method names<-,PDict-method [[,PDict-method duplicated,PDict-method patternFrequency patternFrequency,PDict-method class:TB_PDict TB_PDict-class TB_PDict head,TB_PDict-method tb,TB_PDict-method tb.width,TB_PDict-method tail,TB_PDict-method show,TB_PDict-method class:MTB_PDict MTB_PDict-class MTB_PDict as.list,MTB_PDict-method show,MTB_PDict-method PDict PDict,character-method PDict,DNAStringSet-method PDict,XStringViews-method PDict,AsIs-method
Keywords: methods classes
Description: PDict objects
URL: ../../../library/Biostrings/html/PDict-class.html

Entry: PairwiseAlignedXStringSet-class
Aliases: class:PairwiseAlignedXStringSet PairwiseAlignedXStringSet-class PairwiseAlignedXStringSet class:PairwiseAlignedFixedSubject PairwiseAlignedFixedSubject-class PairwiseAlignedFixedSubject class:PairwiseAlignedFixedSubjectSummary PairwiseAlignedFixedSubjectSummary-class PairwiseAlignedFixedSubjectSummary PairwiseAlignedXStringSet,XString,XString-method PairwiseAlignedXStringSet,XStringSet,missing-method PairwiseAlignedXStringSet,character,missing-method PairwiseAlignedXStringSet,character,character-method PairwiseAlignedFixedSubject,XString,XString-method PairwiseAlignedFixedSubject,XStringSet,missing-method PairwiseAlignedFixedSubject,character,missing-method PairwiseAlignedFixedSubject,character,character-method pattern,PairwiseAlignedXStringSet-method subject,PairwiseAlignedXStringSet-method type type,PairwiseAlignedXStringSet-method score,PairwiseAlignedXStringSet-method nindel,PairwiseAlignedXStringSet-method length,PairwiseAlignedXStringSet-method nchar,PairwiseAlignedXStringSet-method xsbasetype,PairwiseAlignedXStringSet-method show,PairwiseAlignedXStringSet-method [,PairwiseAlignedXStringSet-method [<-,PairwiseAlignedXStringSet-method rep,PairwiseAlignedXStringSet-method summary,PairwiseAlignedFixedSubject-method Views,PairwiseAlignedFixedSubject-method aligned,PairwiseAlignedFixedSubject-method as.character,PairwiseAlignedFixedSubject-method toString,PairwiseAlignedFixedSubject-method as.matrix,PairwiseAlignedFixedSubject-method type,PairwiseAlignedFixedSubjectSummary-method score,PairwiseAlignedFixedSubjectSummary-method nindel,PairwiseAlignedFixedSubjectSummary-method length,PairwiseAlignedFixedSubjectSummary-method nchar,PairwiseAlignedFixedSubjectSummary-method show,PairwiseAlignedFixedSubjectSummary-method
Keywords: methods classes
Description: PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
URL: ../../../library/Biostrings/html/PairwiseAlignedXStringSet-class.html

Entry: QualityScaledXStringSet-class
Aliases: class:QualityScaledXStringSet QualityScaledXStringSet-class QualityScaledXStringSet class:QualityScaledBStringSet QualityScaledBStringSet-class QualityScaledBStringSet class:QualityScaledDNAStringSet QualityScaledDNAStringSet-class QualityScaledDNAStringSet class:QualityScaledRNAStringSet QualityScaledRNAStringSet-class QualityScaledRNAStringSet class:QualityScaledAAStringSet QualityScaledAAStringSet-class QualityScaledAAStringSet quality quality,QualityScaledXStringSet-method narrow,QualityScaledXStringSet-method append,QualityScaledXStringSet,QualityScaledXStringSet-method show,QualityScaledXStringSet-method [,QualityScaledXStringSet-method
Keywords: methods classes
Description: QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
URL: ../../../library/Biostrings/html/QualityScaledXStringSet-class.html

Entry: RNAString-class
Aliases: class:RNAString RNAString-class RNA_BASES RNA_ALPHABET RNAString
Keywords: methods classes
Description: RNAString objects
URL: ../../../library/Biostrings/html/RNAString-class.html

Entry: XString-class
Aliases: class:XString XString-class class:BString BString-class XString BString alphabet alphabet,ANY-method length,XString-method nchar,XString-method xsbasetype,BString-method xsbasetype,DNAString-method xsbasetype,RNAString-method xsbasetype,AAString-method xsbasetype<-,XString-method coerce,XString,BString-method coerce,XString,DNAString-method coerce,XString,RNAString-method coerce,XString,AAString-method coerce,character,BString-method coerce,character,DNAString-method coerce,character,RNAString-method coerce,character,AAString-method coerce,character,XString-method as.character,XString-method toString,XString-method show,XString-method [,XString-method ==,XString,XString-method ==,BString,character-method ==,character,BString-method !=,XString,XString-method !=,BString,character-method !=,character,BString-method
Keywords: methods classes
Description: BString objects
URL: ../../../library/Biostrings/html/XString-class.html

Entry: XStringPartialMatches-class
Aliases: class:XStringPartialMatches XStringPartialMatches-class subpatterns subpatterns,XStringPartialMatches-method pattern pattern,XStringPartialMatches-method show,XStringPartialMatches-method [,XStringPartialMatches-method
Keywords: methods classes
Description: XStringPartialMatches objects
URL: ../../../library/Biostrings/html/XStringPartialMatches-class.html

Entry: XStringQuality-class
Aliases: class:XStringQuality XStringQuality-class XStringQuality class:PhredQuality PhredQuality-class PhredQuality class:SolexaQuality SolexaQuality-class SolexaQuality coerce,character,PhredQuality-method coerce,BString,PhredQuality-method coerce,BStringSet,PhredQuality-method coerce,integer,PhredQuality-method coerce,numeric,PhredQuality-method coerce,PhredQuality,integer-method as.integer,PhredQuality-method coerce,PhredQuality,numeric-method as.numeric,PhredQuality-method coerce,character,SolexaQuality-method coerce,BString,SolexaQuality-method coerce,BStringSet,SolexaQuality-method coerce,integer,SolexaQuality-method coerce,numeric,SolexaQuality-method coerce,SolexaQuality,integer-method as.integer,SolexaQuality-method coerce,SolexaQuality,numeric-method as.numeric,SolexaQuality-method
Keywords: methods classes
Description: PhredQuality and SolexaQuality objects
URL: ../../../library/Biostrings/html/XStringQuality-class.html

Entry: XStringSet-class
Aliases: class:XStringSet XStringSet-class XStringSet class:BStringSet BStringSet-class BStringSet class:DNAStringSet DNAStringSet-class DNAStringSet class:RNAStringSet RNAStringSet-class RNAStringSet class:AAStringSet AAStringSet-class AAStringSet length,XStringSet-method width,character-method width,XStringSet-method nchar,XStringSet-method names,XStringSet-method names<-,XStringSet-method narrow,character-method narrow,XStringSet-method subseq,character-method subseq,XStringSet-method threebands,character-method threebands,XStringSet-method subseq<-,character-method subseq<-,XStringSet-method xsbasetype,XStringSet-method xsbasetype<-,XStringSet-method coerce,XStringSet,BStringSet-method coerce,XStringSet,DNAStringSet-method coerce,XStringSet,RNAStringSet-method coerce,XStringSet,AAStringSet-method coerce,character,BStringSet-method coerce,character,DNAStringSet-method coerce,character,RNAStringSet-method coerce,character,AAStringSet-method coerce,character,XStringSet-method coerce,XString,BStringSet-method coerce,XString,DNAStringSet-method coerce,XString,RNAStringSet-method coerce,XString,AAStringSet-method coerce,XString,XStringSet-method show,XStringSet-method [,XStringSet-method rep,XStringSet-method [[,XStringSet-method [[<-,XStringSet-method append,XStringSet,XStringSet-method order,XStringSet-method sort,XStringSet-method rank,XStringSet-method duplicated,XStringSet-method unique,XStringSet-method union,XStringSet,XStringSet-method intersect,XStringSet,XStringSet-method setdiff,XStringSet,XStringSet-method setequal,XStringSet,XStringSet-method %in%,character,XStringSet-method %in%,XString,XStringSet-method %in%,XStringSet,XStringSet-method match,character,XStringSet-method match,XString,XStringSet-method match,XStringSet,XStringSet-method unlist,XStringSet-method as.character,XStringSet-method toString,XStringSet-method as.matrix,XStringSet-method
Keywords: methods classes
Description: BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects
URL: ../../../library/Biostrings/html/XStringSet-class.html

Entry: XStringSet-io
Aliases: read.XStringViews read.BStringSet read.DNAStringSet read.RNAStringSet read.AAStringSet write.XStringSet write.XStringViews fastq.geometry FASTArecordsToCharacter CharacterToFASTArecords FASTArecordsToXStringViews XStringSetToFASTArecords read.BStringViews write.BStringViews FASTArecordsToBStringViews
Keywords: utilities manip
Description: Read/write an XStringSet or XStringViews object from/to a file
URL: ../../../library/Biostrings/html/XStringSet-io.html

Entry: XStringViews-class
Aliases: class:XStringViews XStringViews-class Views,XString-method Views,character-method nchar,XStringViews-method xsbasetype,XStringViews-method xsbasetype<-,XStringViews-method coerce,XStringViews,XStringSet-method coerce,XStringViews,BStringSet-method coerce,XStringViews,DNAStringSet-method coerce,XStringViews,RNAStringSet-method coerce,XStringViews,AAStringSet-method show,XStringViews-method ==,XStringViews,XStringViews-method ==,XStringViews,XString-method ==,XStringViews,character-method ==,XString,XStringViews-method ==,character,XStringViews-method !=,XStringViews,XStringViews-method !=,XStringViews,XString-method !=,XStringViews,character-method !=,XString,XStringViews-method !=,character,XStringViews-method as.character,XStringViews-method as.matrix,XStringViews-method toString,XStringViews-method
Keywords: methods classes
Description: The XStringViews class
URL: ../../../library/Biostrings/html/XStringViews-class.html

Entry: XStringViews-constructors
Aliases: XStringViews-constructors adjacentViews XStringViews XStringViews,ANY-method XStringViews,XString-method XStringViews,XStringViews-method BStringViews BStringViews,ANY-method BStringViews,file-method BStringViews,XString-method BStringViews,XStringViews-method
Keywords: methods
Description: Basic functions for creating or modifying XStringViews objects
URL: ../../../library/Biostrings/html/XStringViews-constructors.html

Entry: align-utils
Aliases: align-utils mismatch,AlignedXStringSet0,missing-method nmatch,PairwiseAlignedXStringSet,missing-method nmatch,PairwiseAlignedFixedSubjectSummary,missing-method nmismatch,AlignedXStringSet0,missing-method nmismatch,PairwiseAlignedXStringSet,missing-method nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method nedit nedit,PairwiseAlignedXStringSet-method nedit,PairwiseAlignedFixedSubjectSummary-method mismatchTable mismatchTable,AlignedXStringSet0-method mismatchTable,QualityAlignedXStringSet-method mismatchTable,PairwiseAlignedXStringSet-method mismatchSummary mismatchSummary,AlignedXStringSet0-method mismatchSummary,QualityAlignedXStringSet-method mismatchSummary,PairwiseAlignedFixedSubject-method mismatchSummary,PairwiseAlignedFixedSubjectSummary-method coverage,AlignedXStringSet0-method coverage,PairwiseAlignedFixedSubject-method coverage,PairwiseAlignedFixedSubjectSummary-method compareStrings compareStrings,character,character-method compareStrings,XString,XString-method compareStrings,XStringSet,XStringSet-method compareStrings,AlignedXStringSet0,AlignedXStringSet0-method compareStrings,PairwiseAlignedXStringSet,missing-method consensusMatrix,PairwiseAlignedFixedSubject-method
Keywords: methods
Description: Utility functions related to sequence alignment
URL: ../../../library/Biostrings/html/align-utils.html

Entry: basecontent
Aliases: basecontent countbases
Keywords: manip
Description: Obtain the ATCG content of a gene
URL: ../../../library/Biostrings/html/basecontent.html

Entry: chartr
Aliases: chartr,ANY,ANY,XString-method chartr,ANY,ANY,XStringSet-method chartr,ANY,ANY,XStringViews-method chartr,ANY,ANY,MaskedXString-method
Keywords: methods manip
Description: Translating letters of a sequence
URL: ../../../library/Biostrings/html/chartr.html

Entry: complementSeq
Aliases: complementSeq
Keywords: manip
Description: Complementary sequence.
URL: ../../../library/Biostrings/html/complementSeq.html

Entry: findPalindromes
Aliases: findPalindromes findPalindromes,XString-method findPalindromes,XStringViews-method findPalindromes,MaskedXString-method palindromeArmLength palindromeArmLength,XString-method palindromeArmLength,XStringViews-method palindromeLeftArm palindromeLeftArm,XString-method palindromeLeftArm,XStringViews-method palindromeRightArm palindromeRightArm,XString-method palindromeRightArm,XStringViews-method findComplementedPalindromes findComplementedPalindromes,DNAString-method findComplementedPalindromes,XStringViews-method findComplementedPalindromes,MaskedXString-method complementedPalindromeArmLength complementedPalindromeArmLength,DNAString-method complementedPalindromeArmLength,XStringViews-method complementedPalindromeLeftArm complementedPalindromeLeftArm,DNAString-method complementedPalindromeLeftArm,XStringViews-method complementedPalindromeRightArm complementedPalindromeRightArm,DNAString-method complementedPalindromeRightArm,XStringViews-method
Keywords: methods
Description: Searching a sequence for palindromes or complemented palindromes
URL: ../../../library/Biostrings/html/findPalindromes.html

Entry: gregexpr2
Aliases: gregexpr2
Keywords: manip
Description: A replacement for R standard gregexpr function
URL: ../../../library/Biostrings/html/gregexpr2.html

Entry: injectHardMask
Aliases: injectHardMask injectHardMask,XStringViews-method injectHardMask,MaskedXString-method
Keywords: utilities manip
Description: Injecting a hard mask in a sequence
URL: ../../../library/Biostrings/html/injectHardMask.html

Entry: letter
Aliases: letter letter,character-method letter,XString-method letter,XStringViews-method letter,MaskedXString-method
Keywords: methods
Description: Subsetting a string
URL: ../../../library/Biostrings/html/letter.html

Entry: letterFrequency
Aliases: letterFrequency alphabetFrequency alphabetFrequency,XString-method alphabetFrequency,DNAString-method alphabetFrequency,RNAString-method alphabetFrequency,XStringSet-method alphabetFrequency,DNAStringSet-method alphabetFrequency,RNAStringSet-method alphabetFrequency,XStringViews-method alphabetFrequency,MaskedXString-method hasOnlyBaseLetters hasOnlyBaseLetters,DNAString-method hasOnlyBaseLetters,DNAStringSet-method hasOnlyBaseLetters,RNAString-method hasOnlyBaseLetters,RNAStringSet-method hasOnlyBaseLetters,XStringViews-method hasOnlyBaseLetters,MaskedDNAString-method hasOnlyBaseLetters,MaskedRNAString-method uniqueLetters uniqueLetters,XString-method uniqueLetters,XStringSet-method uniqueLetters,XStringViews-method uniqueLetters,MaskedXString-method consensusMatrix consensusMatrix,character-method consensusMatrix,matrix-method consensusMatrix,list-method consensusMatrix,XStringSet-method consensusMatrix,XStringViews-method consensusString consensusString,matrix-method consensusString,XStringSet-method consensusString,XStringViews-method consensusString,ANY-method consmat consmat,ANY-method
Keywords: methods manip
Description: Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
URL: ../../../library/Biostrings/html/letterFrequency.html

Entry: longestConsecutive
Aliases: longestConsecutive
Keywords: manip
Description: Obtain the length of the longest substring containing only 'letter'
URL: ../../../library/Biostrings/html/longestConsecutive.html

Entry: maskMotif
Aliases: maskMotif maskMotif,MaskedXString,XString-method maskMotif,MaskedXString,character-method maskMotif,XString,ANY-method mask
Keywords: methods manip
Description: Masking by content (or by position)
URL: ../../../library/Biostrings/html/maskMotif.html

Entry: match-utils
Aliases: match-utils neditStartingAt neditEndingAt neditAt isMatchingStartingAt isMatchingEndingAt isMatchingAt neditStartingAt,character-method neditStartingAt,XString-method neditStartingAt,XStringSet-method neditEndingAt,character-method neditEndingAt,XString-method neditEndingAt,XStringSet-method isMatchingStartingAt,character-method isMatchingStartingAt,XString-method isMatchingStartingAt,XStringSet-method isMatchingEndingAt,character-method isMatchingEndingAt,XString-method isMatchingEndingAt,XStringSet-method hasLetterAt mismatch mismatch,ANY,XStringViews-method nmatch nmatch,ANY,XStringViews-method nmismatch nmismatch,ANY,XStringViews-method coverage,MaskedXString-method coverage,MIndex-method nmismatchStartingAt nmismatchEndingAt isMatching
Keywords: methods
Description: Utility functions related to pattern matching
URL: ../../../library/Biostrings/html/match-utils.html

Entry: matchLRPatterns
Aliases: matchLRPatterns matchLRPatterns,XString-method matchLRPatterns,XStringViews-method matchLRPatterns,MaskedXString-method
Keywords: methods
Description: Find paired matches in a sequence
URL: ../../../library/Biostrings/html/matchLRPatterns.html

Entry: matchPDict
Aliases: matchPDict-exact matchPDict matchPDict,XString-method matchPDict,XStringSet-method matchPDict,XStringViews-method matchPDict,MaskedXString-method countPDict countPDict,XString-method countPDict,XStringSet-method countPDict,XStringViews-method countPDict,MaskedXString-method whichPDict whichPDict,XString-method vmatchPDict vmatchPDict,ANY-method vmatchPDict,XString-method vmatchPDict,MaskedXString-method vcountPDict vcountPDict,XString-method vcountPDict,XStringSet-method vcountPDict,XStringViews-method vcountPDict,MaskedXString-method extractAllMatches
Keywords: methods
Description: Searching a sequence for patterns stored in a preprocessed dictionary
URL: ../../../library/Biostrings/html/matchPDict-exact.html

Entry: matchPDict-inexact
Aliases: matchPDict-inexact
Keywords: methods
Description: Inexact matching with matchPDict()/countPDict()/whichPDict()
URL: ../../../library/Biostrings/html/matchPDict-inexact.html

Entry: matchPWM
Aliases: maxWeights maxScore PWMscoreStartingAt matchPWM countPWM reverseComplement,matrix-method PWMscore
Keywords: methods manip utilities
Description: A simple PWM matching function and related utilities
URL: ../../../library/Biostrings/html/matchPWM.html

Entry: matchPattern
Aliases: matchPattern matchPattern,character-method matchPattern,XString-method matchPattern,XStringSet-method matchPattern,XStringViews-method matchPattern,MaskedXString-method countPattern countPattern,character-method countPattern,XString-method countPattern,XStringSet-method countPattern,XStringViews-method countPattern,MaskedXString-method vmatchPattern vmatchPattern,character-method vmatchPattern,XString-method vmatchPattern,XStringSet-method vmatchPattern,XStringViews-method vmatchPattern,MaskedXString-method vcountPattern vcountPattern,character-method vcountPattern,XString-method vcountPattern,XStringSet-method vcountPattern,XStringViews-method vcountPattern,MaskedXString-method matchDNAPattern
Keywords: methods
Description: String searching functions
URL: ../../../library/Biostrings/html/matchPattern.html

Entry: matchProbePair
Aliases: matchProbePair matchProbePair,DNAString-method matchProbePair,XStringViews-method matchProbePair,MaskedDNAString-method
Keywords: methods
Description: Find "theoretical amplicons" mapped to a probe pair
URL: ../../../library/Biostrings/html/matchProbePair.html

Entry: matchprobes
Aliases: matchprobes
Keywords: manip
Description: A function to match a query sequence to the sequences of a set of probes.
URL: ../../../library/Biostrings/html/matchprobes.html

Entry: needwunsQS
Aliases: needwunsQS needwunsQS,character,character-method needwunsQS,character,XString-method needwunsQS,XString,character-method needwunsQS,XString,XString-method print.needwunsQS alignScore.needwunsQS alignScore
Keywords: models methods
Description: (Deprecated) Needleman-Wunsch Global Alignment
URL: ../../../library/Biostrings/html/needwunsQS.html

Entry: nucleotideFrequency
Aliases: oligonucleotideFrequency oligonucleotideFrequency oligonucleotideFrequency,XString-method oligonucleotideFrequency,XStringSet-method oligonucleotideFrequency,XStringViews-method oligonucleotideFrequency,MaskedXString-method dinucleotideFrequency trinucleotideFrequency nucleotideFrequencyAt nucleotideFrequencyAt,XStringSet-method nucleotideFrequencyAt,XStringViews-method oligonucleotideTransitions mkAllStrings
Keywords: methods manip
Description: Calculate the frequency of oligonucleotides in a DNA or RNA sequence, plus some related functions
URL: ../../../library/Biostrings/html/nucleotideFrequency.html

Entry: pairwiseAlignment
Aliases: pairwiseAlignment pairwiseAlignment,character,character-method pairwiseAlignment,character,XString-method pairwiseAlignment,character,XStringSet-method pairwiseAlignment,character,QualityScaledXStringSet-method pairwiseAlignment,XString,character-method pairwiseAlignment,XString,XString-method pairwiseAlignment,XString,XStringSet-method pairwiseAlignment,XString,QualityScaledXStringSet-method pairwiseAlignment,XStringSet,character-method pairwiseAlignment,XStringSet,XString-method pairwiseAlignment,XStringSet,XStringSet-method pairwiseAlignment,XStringSet,QualityScaledXStringSet-method pairwiseAlignment,QualityScaledXStringSet,character-method pairwiseAlignment,QualityScaledXStringSet,XString-method pairwiseAlignment,QualityScaledXStringSet,XStringSet-method pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method
Keywords: models methods
Description: Optimal Pairwise Alignment
URL: ../../../library/Biostrings/html/pairwiseAlignment.html

Entry: phiX174Phage
Aliases: phiX174Phage srPhiX174 quPhiX174 wtPhiX174
Keywords: datasets
Description: Versions of bacteriophage phiX174 complete genome and sample short reads
URL: ../../../library/Biostrings/html/phiX174Phage.html

Entry: pid
Aliases: pid pid,PairwiseAlignedXStringSet-method
Keywords: methods
Description: Percent Sequence Identity
URL: ../../../library/Biostrings/html/pid.html

Entry: pmatchPattern
Aliases: lcprefix lcprefix,character,character-method lcprefix,character,XString-method lcprefix,XString,character-method lcprefix,XString,XString-method lcsuffix lcsuffix,character,character-method lcsuffix,character,XString-method lcsuffix,XString,character-method lcsuffix,XString,XString-method lcsubstr lcsubstr,character,character-method lcsubstr,character,XString-method lcsubstr,XString,character-method lcsubstr,XString,XString-method pmatchPattern pmatchPattern,character-method pmatchPattern,XString-method pmatchPattern,XStringViews-method
Keywords: methods
Description: Longest Common Prefix/Suffix/Substring searching functions
URL: ../../../library/Biostrings/html/pmatchPattern.html

Entry: readFASTA
Aliases: fasta.info readFASTA writeFASTA
Keywords: utilities manip
Description: Functions to read/write FASTA formatted files
URL: ../../../library/Biostrings/html/readFASTA.html

Entry: replaceLetterAt
Aliases: replaceLetterAt replaceLetterAt,DNAString-method replaceLetterAt,DNAStringSet-method .inplaceReplaceLetterAt replaceLetterAtLoc
Keywords: utilities manip
Description: Replacing letters in a sequence (or set of sequences) at some specified locations
URL: ../../../library/Biostrings/html/replaceLetterAt.html

Entry: reverseComplement
Aliases: reverse,character-method reverse,XString-method reverse,XStringSet-method reverse,XStringViews-method reverse,MaskedXString-method complement complement,DNAString-method complement,RNAString-method complement,DNAStringSet-method complement,RNAStringSet-method complement,XStringViews-method complement,MaskedDNAString-method complement,MaskedRNAString-method reverseComplement reverseComplement,DNAString-method reverseComplement,RNAString-method reverseComplement,DNAStringSet-method reverseComplement,RNAStringSet-method reverseComplement,XStringViews-method reverseComplement,MaskedDNAString-method reverseComplement,MaskedRNAString-method strrev
Keywords: methods manip
Description: Sequence reversing and complementing
URL: ../../../library/Biostrings/html/reverse.html

Entry: reverseSeq
Aliases: reverseSeq revcompDNA revcompRNA
Keywords: manip
Description: Reverse Sequence
URL: ../../../library/Biostrings/html/reverseSeq.html

Entry: stringDist
Aliases: stringDist stringDist,character-method stringDist,XStringSet-method stringDist,QualityScaledXStringSet-method
Keywords: character multivariate cluster
Description: String Distance/Alignment Score Matrix
URL: ../../../library/Biostrings/html/stringDist.html

Entry: subXString
Aliases: subXString subBString substr,XString-method substr,MaskedXString-method substring,XString-method substring,MaskedXString-method
Keywords: methods manip
Description: Fast substring extraction
URL: ../../../library/Biostrings/html/subXString.html

Entry: substitution.matrices
Aliases: substitution.matrices BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 BLOSUM100 PAM30 PAM40 PAM70 PAM120 PAM250 nucleotideSubstitutionMatrix qualitySubstitutionMatrices errorSubstitutionMatrices
Keywords: utilities data datasets
Description: Scoring matrices
URL: ../../../library/Biostrings/html/substitution_matrices.html

Entry: toComplex
Aliases: toComplex toComplex,DNAString-method as.complex,DNAString-method
Keywords: methods
Description: Turning a DNA sequence into a vector of complex numbers
URL: ../../../library/Biostrings/html/toComplex.html

Entry: translate
Aliases: transcribe cDNA dna2rna rna2dna codons codons,DNAString-method codons,RNAString-method codons,MaskedDNAString-method codons,MaskedRNAString-method translate translate,DNAString-method translate,RNAString-method translate,DNAStringSet-method translate,RNAStringSet-method translate,MaskedDNAString-method translate,MaskedRNAString-method
Keywords: methods manip
Description: DNA/RNA transcription and translation
URL: ../../../library/Biostrings/html/translate.html

Entry: trimLRPatterns
Aliases: trimLRPatterns trimLRPatterns,XString-method trimLRPatterns,XStringSet-method
Keywords: methods
Description: Trim Flanking Patterns from Sequences
URL: ../../../library/Biostrings/html/trimLRPatterns.html

Entry: xscat
Aliases: xscat
Keywords: methods manip
Description: Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
URL: ../../../library/Biostrings/html/xscat.html

Entry: yeastSEQCHR1
Aliases: yeastSEQCHR1
Keywords: datasets
Description: An annotation data file for CHR1 in the yeastSEQ package
URL: ../../../library/Biostrings/html/yeastSEQCHR1.html
