Entry: AAString-class
Aliases: class:AAString AAString-class AA_ALPHABET AAString alphabet,AAString-method
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: 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:SparseList SparseList-class SparseList length,SparseList-method ls,SparseList-method as.list,SparseList-method [[,SparseList-method show,externalptr-method class:XRaw XRaw-class XRaw length,XRaw-method as.integer,XRaw-method toString,XRaw-method initialize,XRaw-method show,XRaw-method ==,XRaw,XRaw-method !=,XRaw,XRaw-method [,XRaw-method [<-,XRaw-method class:PrintableXRaw PrintableXRaw-class PrintableXRaw show,PrintableXRaw-method [,PrintableXRaw-method class:XInteger XInteger-class XInteger length,XInteger-method as.integer,XInteger-method initialize,XInteger-method show,XInteger-method ==,XInteger,XInteger-method !=,XInteger,XInteger-method [,XInteger-method [<-,XInteger-method class:XStringCodec XStringCodec-class XStringCodec initialize,XStringCodec-method alphabet,XStringCodec-method
Keywords: internal methods classes
Description: Biostrings internals
URL: ../../../library/Biostrings/html/Biostrings-internals.html

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

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

Entry: IRanges-class
Aliases: class:IRanges IRanges-class IRanges class:UnlockedIRanges UnlockedIRanges-class UnlockedIRanges class:Views Views-class Views class:LockedIRanges LockedIRanges-class LockedIRanges class:NormalIRanges NormalIRanges-class NormalIRanges length,IRanges-method start,IRanges-method width width,IRanges-method end,IRanges-method names,IRanges-method desc isNormal isNormal,IRanges-method whichFirstNotNormal whichFirstNotNormal,IRanges-method isEmpty isEmpty,IRanges-method isEmpty,NormalIRanges-method max,NormalIRanges-method min,NormalIRanges-method initialize,IRanges-method initialize,Views-method initialize,NormalIRanges-method IRanges coerce,IRanges,NormalIRanges-method coerce,UnlockedIRanges,NormalIRanges-method coerce,Views,NormalIRanges-method coerce,LockedIRanges,NormalIRanges-method as.data.frame,IRanges-method show,IRanges-method [,IRanges-method [<-,IRanges-method duplicated,IRanges-method as.matrix,IRanges-method start<- start<-,UnlockedIRanges-method width<- width<-,UnlockedIRanges-method end<- end<-,UnlockedIRanges-method names<-,IRanges-method desc<- update,UnlockedIRanges-method first first,IRanges-method last last,IRanges-method
Keywords: methods classes
Description: IRanges and NormalIRanges objects
URL: ../../../library/Biostrings/html/IRanges-class.html

Entry: IRanges-utils
Aliases: IRanges-utils intToRanges intToAdjacentRanges shift shift,IRanges-method restrict restrict,IRanges-method narrow narrow,IRanges-method narrow,NormalIRanges-method narrow,numeric-method reduce reduce,IRanges-method toNormalIRanges gaps gaps,IRanges-method
Keywords: utilities
Description: IRanges utility functions
URL: ../../../library/Biostrings/html/IRanges-utils.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: MaskCollection-class
Aliases: class:MaskCollection MaskCollection-class MaskCollection nir_list nir_list,MaskCollection-method length,MaskCollection-method width,MaskCollection-method active active,MaskCollection-method active<- active<-,MaskCollection-method names,MaskCollection-method names<-,MaskCollection-method Mask isEmpty,MaskCollection-method max,MaskCollection-method min,MaskCollection-method maskedwidth maskedwidth,MaskCollection-method maskedratio maskedratio,MaskCollection-method [[,MaskCollection-method [[<-,MaskCollection-method [,MaskCollection-method [<-,MaskCollection-method append,MaskCollection-method narrow,MaskCollection-method reduce,MaskCollection-method gaps,MaskCollection-method coerce,MaskCollection,NormalIRanges-method show,MaskCollection-method
Keywords: methods classes
Description: MaskCollection objects
URL: ../../../library/Biostrings/html/MaskCollection-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 alphabet,MaskedXString-method length,MaskedXString-method maskedwidth,MaskedXString-method maskedratio,MaskedXString-method nchar,MaskedXString-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 XString,MaskedXString-method coerce,MaskedXString,MaskCollection-method coerce,MaskedXString,NormalIRanges-method coerce,MaskedXString,XStringViews-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
Keywords: methods classes
Description: MaskedXString objects
URL: ../../../library/Biostrings/html/MaskedXString-class.html

Entry: PDict-class
Aliases: class:ACtree ACtree-class ACtree length,ACtree-method show,ACtree-method [,ACtree-method as.matrix,ACtree-method initialize,ACtree-method class:Dups Dups-class Dups length,Dups-method duplicated,Dups-method class:PDict PDict-class patternFrequency class:CWdna_PDict CWdna_PDict-class CWdna_PDict initialize,CWdna_PDict-method length,CWdna_PDict-method width,CWdna_PDict-method names,CWdna_PDict-method show,CWdna_PDict-method duplicated,CWdna_PDict-method patternFrequency,CWdna_PDict-method class:TBdna_PDict TBdna_PDict-class TBdna_PDict initialize,TBdna_PDict-method head,TBdna_PDict-method tail,TBdna_PDict-method show,TBdna_PDict-method duplicated,TBdna_PDict-method patternFrequency,TBdna_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: RNAString-class
Aliases: class:RNAString RNAString-class RNA_ALPHABET RNAString alphabet,RNAString-method
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 XString,character-method XString,AsIs-method XString,XString-method BString alphabet alphabet,BString-method length,XString-method nchar,XString-method as.character,XString-method toString,XString-method show,XString-method subseq subseq,XString-method [,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: XStringAlign-class
Aliases: class:XStringAlign XStringAlign-class XStringAlign initialize,XStringAlign-method align1 align1,XStringAlign-method align2 align2,XStringAlign-method type type,XStringAlign-method score score,XStringAlign-method length,XStringAlign-method nchar,XStringAlign-method alphabet,XStringAlign-method show,XStringAlign-method as.character,XStringAlign-method
Keywords: methods classes
Description: XStringAlign objects
URL: ../../../library/Biostrings/html/XStringAlign-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: 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 class:XStringList XStringList-class XStringList class:BStringList BStringList-class BStringList class:DNAStringList DNAStringList-class DNAStringList class:RNAStringList RNAStringList-class RNAStringList class:AAStringList AAStringList-class AAStringList nchar,XStringSet-method alphabet,XStringSet-method length,XStringList-method nchar,XStringList-method width,XStringList-method names,XStringList-method names<-,XStringList-method initialize,XStringSet-method XStringSet,character-method XStringSet,AsIs-method XStringSet,XString-method XStringSet,XStringSet-method XStringSet,XStringViews-method BStringSet DNAStringSet RNAStringSet AAStringSet initialize,BStringList-method initialize,DNAStringList-method initialize,RNAStringList-method initialize,AAStringList-method BStringList,character-method DNAStringList,character-method RNAStringList,character-method AAStringList,character-method BStringList,XStringList-method DNAStringList,XStringList-method RNAStringList,XStringList-method AAStringList,XStringList-method BStringList,vector-method DNAStringList,vector-method RNAStringList,vector-method AAStringList,vector-method BStringList,ANY-method DNAStringList,ANY-method RNAStringList,ANY-method AAStringList,ANY-method show,XStringSet-method [[,XStringSet-method [[<-,XStringSet-method as.list,XStringSet-method as.character,XStringSet-method show,XStringList-method [,XStringList-method [<-,XStringList-method [[,XStringList-method [[<-,XStringList-method as.list,XStringList-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 FASTArecordsToCharacter CharacterToFASTArecords FASTArecordsToXStringViews XStringSetToFASTArecords read.BStringViews write.BStringViews FASTArecordsToBStringViews
Keywords: 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 initialize,XStringViews-method subject subject,XStringViews-method alphabet,XStringViews-method width<-,XStringViews-method nchar,XStringViews-method show,XStringViews-method [[,XStringViews-method [[<-,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 as.list,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 views adjacentViews XStringViews XStringViews,ANY-method XStringViews,file-method XStringViews,XString-method XStringViews,XStringViews-method restrict,XStringViews-method trim narrow,XStringViews-method subviews gaps,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: consmat consmat,character-method consmat,matrix-method consmat,list-method consmat,XStringSet-method consmat,XStringViews-method consmat,XStringAlign-method
Keywords: methods
Description: Utility functions related to sequence alignment
URL: ../../../library/Biostrings/html/align-utils.html

Entry: alphabetFrequency
Aliases: 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 oligonucleotideFrequency oligonucleotideFrequency,DNAString-method oligonucleotideFrequency,RNAString-method oligonucleotideFrequency,XStringSet-method oligonucleotideFrequency,XStringViews-method oligonucleotideFrequency,MaskedXString-method dinucleotideFrequency trinucleotideFrequency strrev mkAllStrings
Keywords: category
Description: Functions to calculate the frequency of letters in a biological sequence
URL: ../../../library/Biostrings/html/alphabetFrequency.html

Entry: chartr
Aliases: chartr chartr,XString-method chartr,XStringSet-method chartr,XStringViews-method chartr,MaskedXString-method
Keywords: methods manip
Description: Translating letters of a sequence
URL: ../../../library/Biostrings/html/chartr.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: 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 nmismatchStartingAt nmismatchEndingAt nmismatchStartingAt,character-method nmismatchEndingAt,character-method nmismatchStartingAt,XString-method nmismatchEndingAt,XString-method isMatching isMatching,character-method isMatching,XString-method mismatch mismatch,XStringViews-method coverage coverage,IRanges-method coverage,MaskCollection-method coverage,XStringViews-method coverage,MaskedXString-method coverage,MIndex-method
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 patterns defined by a left and a right part in a sequence
URL: ../../../library/Biostrings/html/matchLRPatterns.html

Entry: matchPDict
Aliases: matchPDict-exact MIndex class:MIndex MIndex-class class:ByPos_MIndex ByPos_MIndex-class class:ByName_MIndex ByName_MIndex-class startIndex startIndex,MIndex-method endIndex countIndex countIndex,MIndex-method [[,MIndex-method $,MIndex-method unlist unlist,MIndex-method length,ByPos_MIndex-method names,ByPos_MIndex-method show,ByPos_MIndex-method [[,ByPos_MIndex-method startIndex,ByPos_MIndex-method endIndex,ByPos_MIndex-method countIndex,ByPos_MIndex-method length,ByName_MIndex-method names,ByName_MIndex-method show,ByName_MIndex-method [[,ByName_MIndex-method startIndex,ByName_MIndex-method endIndex,ByName_MIndex-method countIndex,ByName_MIndex-method matchPDict matchPDict,XString-method matchPDict,XStringViews-method matchPDict,MaskedXString-method countPDict countPDict,XString-method countPDict,XStringViews-method countPDict,MaskedXString-method extractAllMatches
Keywords: methods
Description: Searching a sequence for patterns stored in a dictionary
URL: ../../../library/Biostrings/html/matchPDict-exact.html

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

Entry: matchPWM
Aliases: maxWeights maxScore PWMscore matchPWM countPWM reverseComplement,matrix-method
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,XStringViews-method matchPattern,MaskedXString-method countPattern countPattern,character-method countPattern,XString-method countPattern,XStringViews-method countPattern,MaskedXString-method vcountPattern vcountPattern,character-method vcountPattern,XStringSet-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: 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: pairwiseAlignment
Aliases: pairwiseAlignment pairwiseAlignment,character,character-method pairwiseAlignment,character,XString-method pairwiseAlignment,XString,character-method pairwiseAlignment,XString,XString-method
Keywords: models methods
Description: Optimal Pairwise Alignment
URL: ../../../library/Biostrings/html/pairwiseAlignment.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: read.Mask
Aliases: read.Mask read.agpMask read.gapMask read.liftMask read.rmMask read.trfMask
Keywords: manip
Description: Read a mask from a file
URL: ../../../library/Biostrings/html/read.Mask.html

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

Entry: replaceLetterAtLoc
Aliases: replaceLetterAtLoc replaceLetterAtLoc,DNAString-method .inplaceReplaceLetterAtLoc
Keywords: utilities manip
Description: Replacing letters in a sequence at some specified locations
URL: ../../../library/Biostrings/html/replaceLetterAtLoc.html

Entry: reverseComplement
Aliases: reverse reverse,IRanges-method reverse,NormalIRanges-method reverse,MaskCollection-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 transcribe cDNA dna2rna rna2dna
Keywords: methods manip
Description: Sequence reversing and complementing
URL: ../../../library/Biostrings/html/reverse.html

Entry: subXString
Aliases: subXString subBString substr substr,XString-method substring substring,XString-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
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: Converting a DNAString to a vector of complexes
URL: ../../../library/Biostrings/html/toComplex.html

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