Package: Biostrings 2.73.1

Hervé Pagès

Biostrings: Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Authors:Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Robert Gentleman [aut], Saikat DebRoy [aut], Vince Carey [ctb], Nicolas Delhomme [ctb], Felix Ernst [ctb], Wolfgang Huber [ctb], Beryl Kanali [ctb], Haleema Khan [ctb], Aidan Lakshman [ctb], Kieran O'Neill [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Albert Vill [ctb], Jen Wokaty [ctb], Erik Wright [ctb]

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Biostrings.pdf |Biostrings.html✨
Biostrings/json (API)
NEWS

# Install 'Biostrings' in R:

install.packages('Biostrings', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/biostrings/issues

Datasets:

HNF4alpha - Known HNF4alpha binding sequences
yeastSEQCHR1 - An annotation data file for CHR1 in the yeastSEQ package

On BioConductor:Biostrings-2.73.1(bioc 3.20)Biostrings-2.72.1(bioc 3.19)

bioconductor-package

240 exports 12.79 score 17 dependencies 1149 dependents 220 mentions

Last updated 1 months agofrom:a1fae35686

Exports:.inplaceReplaceLetterAt %in%AA_ALPHABET AA_PROTEINOGENIC AA_STANDARD AAMultipleAlignment AAString AAStringSet AAStringSetList aligned alignedPattern alignedSubject alphabet alphabetFrequency AMINO_ACID_CODE as.data.frame as.list as.matrix BString BStringSet BStringSetList chartr codons coerce collapse colmask colmask<-compareStrings complement computeAllFlinks consensusMatrix consensusString consensusViews countPattern countPDict countPWM coverage deletion detail dinucleotideFrequency dinucleotideFrequencyTest DNA_ALPHABET DNA_BASES DNAMultipleAlignment DNAString DNAStringSet DNAStringSetList duplicated encoding end endIndex errorSubstitutionMatrices extract_character_from_XString_by_positions extract_character_from_XString_by_ranges extractAllMatches extractAt fasta.index fasta.seqlengths fastq.geometry fastq.seqlengths findPalindromes gaps GENETIC_CODE GENETIC_CODE_TABLE get_seqtype_conversion_lookup getGeneticCode getSeq gregexpr2 hasAllFlinks hasLetterAt hasOnlyBaseLetters head IlluminaQuality indel initialize injectHardMask insertion intersect is.unsorted isMatchingAt isMatchingEndingAt isMatchingStartingAt IUPAC_CODE_MAP lcprefix lcsubstr lcsuffix letter letterFrequency letterFrequencyInSlidingView longestConsecutive make_XString_from_string make_XStringSet_from_strings mask maskeddim maskedncol maskednrow maskedratio maskedwidth maskGaps maskMotif masks masks<-match matchLRPatterns matchPattern matchPDict matchProbePair matchprobes matchPWM maxScore maxWeights mergeIUPACLetters minScore minWeights mismatch mismatchSummary mismatchTable mkAllStrings N50 nchar nedit neditAt neditEndingAt neditStartingAt needwunsQS nindel nmatch nmismatch nnodes nucleotideFrequencyAt nucleotideSubstitutionMatrix oligonucleotideFrequency oligonucleotideTransitions order padAndClip pairwiseAlignment PairwiseAlignments PairwiseAlignmentsSingleSubject palindromeArmLength palindromeLeftArm palindromeRightArm parallel_slot_names parallelVectorNames pattern patternFrequency pcompare PDict PhredQuality pid pmatchPattern PWM PWMscoreStartingAt quality QualityScaledAAStringSet QualityScaledBStringSet QualityScaledDNAStringSet QualityScaledRNAStringSet qualitySubstitutionMatrices rank readAAMultipleAlignment readAAStringSet readBStringSet readDNAMultipleAlignment readDNAStringSet readQualityScaledDNAStringSet readRNAMultipleAlignment readRNAStringSet relistToClass replaceAmbiguities replaceAt replaceLetterAt reverse reverseComplement RNA_ALPHABET RNA_BASES RNA_GENETIC_CODE RNAMultipleAlignment RNAString RNAStringSet RNAStringSetList rowmask rowmask<-saveXStringSet seqinfo seqinfo<-seqtype seqtype<-setdiff setequal show showAsCell SolexaQuality sort stackStrings start startIndex stringDist strsplit subpatterns subseq subseq<-substr substring summary tail tb tb.width threebands toComplex toString translate trimLRPatterns trinucleotideFrequency twoWayAlphabetFrequency unaligned union uniqueLetters unitScale unmasked unstrsplit updateObject vcountPattern vcountPDict Views vmatchPattern vmatchPDict vwhichPDict which.isMatchingAt which.isMatchingEndingAt which.isMatchingStartingAt whichPDict width width0 windows write.phylip writePairwiseAlignments writeQualityScaledXStringSet writeXStringSet xscat xscodes

Dependencies:askpass BiocGenerics crayon curl GenomeInfoDb GenomeInfoDbData httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

A short presentation of the basic classes defined in Biostrings 2

Rendered fromBiostrings2Classes.Rnwusingutils::Sweaveon Jul 08 2024.

Last update: 2013-11-01
Started: 2013-11-01

Biostrings Quick Overview

Rendered fromBiostringsQuickOverview.Rnwusingutils::Sweaveon Jul 08 2024.

Last update: 2024-04-23
Started: 2013-11-01

Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment

Wolfgang Huber, Robert Gentleman

Rendered frommatchprobes.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2024-02-12
Started: 2023-04-14

MultipleAlignment Objects

Marc Carlson, Beryl Kanali

Rendered fromMultipleAlignments.Rmdusingknitr::rmarkdownon Jul 08 2024.

Last update: 2024-06-07
Started: 2024-06-07

Pairwise Sequence Alignments

Rendered fromPairwiseAlignments.Rnwusingutils::Sweaveon Jul 08 2024.

Last update: 2024-04-23
Started: 2013-11-01

Help page	Topics
AAString objects	AAString AAString-class AA_ALPHABET AA_PROTEINOGENIC AA_STANDARD class:AAString
The Single-Letter Amino Acid Code	AMINO_ACID_CODE
Replace letters in a sequence or set of sequences	chartr chartr,ANY,ANY,MaskedXString-method chartr,ANY,ANY,XString-method chartr,ANY,ANY,XStringSet-method chartr,ANY,ANY,XStringViews-method replaceAmbiguities
Show (display) detailed object content	detail
Pearson's chi-squared Test and G-tests for String Position Dependence	dinucleotideFrequencyTest dinucleotideFrequencyTest,DNAStringSet-method dinucleotideFrequencyTest,RNAStringSet-method
DNAString objects	class:DNAString DNAString DNAString-class DNA_ALPHABET DNA_BASES
Searching a sequence for palindromes	findPalindromes findPalindromes,DNAString-method findPalindromes,MaskedXString-method findPalindromes,RNAString-method findPalindromes,XString-method findPalindromes,XStringViews-method palindromeArmLength palindromeArmLength,DNAString-method palindromeArmLength,RNAString-method palindromeArmLength,XString-method palindromeArmLength,XStringSet-method palindromeArmLength,XStringViews-method palindromeLeftArm palindromeLeftArm,XString-method palindromeLeftArm,XStringViews-method palindromeRightArm palindromeRightArm,XString-method palindromeRightArm,XStringViews-method
The Standard Genetic Code and its known variants	GENETIC_CODE GENETIC_CODE_TABLE getGeneticCode RNA_GENETIC_CODE
getSeq	getSeq
A replacement for R standard gregexpr function	gregexpr2
Known HNF4alpha binding sequences	HNF4alpha
Injecting a hard mask in a sequence	injectHardMask injectHardMask,MaskedXString-method injectHardMask,XStringViews-method
The IUPAC Extended Genetic Alphabet	IUPAC_CODE_MAP mergeIUPACLetters
Subsetting a string	letter letter,character-method letter,MaskedXString-method letter,XString-method letter,XStringViews-method
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences	alphabetFrequency alphabetFrequency,AAString-method alphabetFrequency,AAStringSet-method alphabetFrequency,DNAString-method alphabetFrequency,DNAStringSet-method alphabetFrequency,MaskedXString-method alphabetFrequency,RNAString-method alphabetFrequency,RNAStringSet-method alphabetFrequency,XString-method alphabetFrequency,XStringSet-method alphabetFrequency,XStringViews-method consensusMatrix consensusMatrix,character-method consensusMatrix,matrix-method consensusMatrix,XStringSet-method consensusMatrix,XStringViews-method consensusString consensusString,ANY-method consensusString,BStringSet-method consensusString,DNAStringSet-method consensusString,matrix-method consensusString,RNAStringSet-method consensusString,XStringViews-method hasOnlyBaseLetters hasOnlyBaseLetters,DNAString-method hasOnlyBaseLetters,DNAStringSet-method hasOnlyBaseLetters,MaskedXString-method hasOnlyBaseLetters,RNAString-method hasOnlyBaseLetters,RNAStringSet-method hasOnlyBaseLetters,XStringViews-method letterFrequency letterFrequency,MaskedXString-method letterFrequency,XString-method letterFrequency,XStringSet-method letterFrequency,XStringViews-method letterFrequencyInSlidingView letterFrequencyInSlidingView,XString-method uniqueLetters uniqueLetters,MaskedXString-method uniqueLetters,XString-method uniqueLetters,XStringSet-method uniqueLetters,XStringViews-method
Obtain the length of the longest substring containing only 'letter'	longestConsecutive
Low-level matching functions	hasLetterAt isMatchingAt isMatchingEndingAt isMatchingEndingAt,character-method isMatchingEndingAt,XString-method isMatchingEndingAt,XStringSet-method isMatchingStartingAt isMatchingStartingAt,character-method isMatchingStartingAt,XString-method isMatchingStartingAt,XStringSet-method lowlevel-matching neditAt neditEndingAt neditEndingAt,character-method neditEndingAt,XString-method neditEndingAt,XStringSet-method neditStartingAt neditStartingAt,character-method neditStartingAt,XString-method neditStartingAt,XStringSet-method which.isMatchingAt which.isMatchingEndingAt which.isMatchingEndingAt,character-method which.isMatchingEndingAt,XString-method which.isMatchingEndingAt,XStringSet-method which.isMatchingStartingAt which.isMatchingStartingAt,character-method which.isMatchingStartingAt,XString-method which.isMatchingStartingAt,XStringSet-method
MaskedXString objects	as.character,MaskedXString-method class:MaskedAAString class:MaskedBString class:MaskedDNAString class:MaskedRNAString class:MaskedXString coerce,AAString,MaskedAAString-method coerce,BString,MaskedBString-method coerce,DNAString,MaskedDNAString-method coerce,MaskedAAString,AAString-method coerce,MaskedBString,BString-method coerce,MaskedDNAString,DNAString-method coerce,MaskedRNAString,RNAString-method coerce,MaskedXString,MaskCollection-method coerce,MaskedXString,MaskedAAString-method coerce,MaskedXString,MaskedBString-method coerce,MaskedXString,MaskedDNAString-method coerce,MaskedXString,MaskedRNAString-method coerce,MaskedXString,NormalIRanges-method coerce,MaskedXString,Views-method coerce,MaskedXString,XStringViews-method coerce,RNAString,MaskedRNAString-method collapse,MaskedXString-method gaps,MaskedXString-method length,MaskedXString-method MaskedAAString MaskedAAString-class MaskedBString MaskedBString-class MaskedDNAString MaskedDNAString-class maskedratio,MaskedXString-method MaskedRNAString MaskedRNAString-class maskedwidth,MaskedXString-method MaskedXString MaskedXString-class masks masks,MaskedXString-method masks,XString-method masks<- masks<-,MaskedXString,MaskCollection-method masks<-,MaskedXString,NULL-method masks<-,XString,ANY-method masks<-,XString,NULL-method nchar,MaskedXString-method seqtype,MaskedXString-method seqtype<-,MaskedXString-method show,MaskedXString-method subseq,MaskedXString-method toString,MaskedXString-method unmasked unmasked,MaskedXString-method unmasked,XString-method Views,MaskedXString-method
Masking by content (or by position)	mask maskMotif maskMotif,MaskedXString,character-method maskMotif,MaskedXString,XString-method maskMotif,XString,ANY-method
Utility functions operating on the matches returned by a high-level matching function	coverage,MaskedXString-method coverage,MIndex-method match-utils mismatch mismatch,ANY,XStringViews-method nmatch nmatch,ANY,XStringViews-method nmismatch nmismatch,ANY,XStringViews-method
Find paired matches in a sequence	matchLRPatterns matchLRPatterns,MaskedXString-method matchLRPatterns,XString-method matchLRPatterns,XStringViews-method
String searching functions	countPattern countPattern,character-method countPattern,MaskedXString-method countPattern,XString-method countPattern,XStringSet-method countPattern,XStringViews-method matchPattern matchPattern,character-method matchPattern,MaskedXString-method matchPattern,XString-method matchPattern,XStringSet-method matchPattern,XStringViews-method vcountPattern vcountPattern,character-method vcountPattern,MaskedXString-method vcountPattern,XString-method vcountPattern,XStringSet-method vcountPattern,XStringViews-method vmatchPattern vmatchPattern,character-method vmatchPattern,MaskedXString-method vmatchPattern,XString-method vmatchPattern,XStringSet-method vmatchPattern,XStringViews-method
Matching a dictionary of patterns against a reference	countPDict countPDict,MaskedXString-method countPDict,XString-method countPDict,XStringSet-method countPDict,XStringViews-method extractAllMatches matchPDict matchPDict,MaskedXString-method matchPDict,XString-method matchPDict,XStringSet-method matchPDict,XStringViews-method matchPDict-exact vcountPDict vcountPDict,MaskedXString-method vcountPDict,XString-method vcountPDict,XStringSet-method vcountPDict,XStringViews-method vmatchPDict vmatchPDict,ANY-method vmatchPDict,MaskedXString-method vmatchPDict,XString-method vwhichPDict vwhichPDict,MaskedXString-method vwhichPDict,XString-method vwhichPDict,XStringSet-method vwhichPDict,XStringViews-method whichPDict whichPDict,MaskedXString-method whichPDict,XString-method whichPDict,XStringSet-method whichPDict,XStringViews-method
Inexact matching with matchPDict()/countPDict()/whichPDict()	matchPDict-inexact
Find "theoretical amplicons" mapped to a probe pair	matchProbePair matchProbePair,DNAString-method matchProbePair,MaskedDNAString-method matchProbePair,XStringViews-method
(Deprecated) A function to match a query sequence to the sequences of a set of probes.	matchprobes
PWM creating, matching, and related utilities	countPWM countPWM,character-method countPWM,DNAString-method countPWM,MaskedDNAString-method countPWM,XStringViews-method matchPWM matchPWM,character-method matchPWM,DNAString-method matchPWM,MaskedDNAString-method matchPWM,XStringViews-method maxScore maxScore,ANY-method maxWeights maxWeights,matrix-method minScore minScore,ANY-method minWeights minWeights,matrix-method PWM PWM,character-method PWM,DNAStringSet-method PWM,matrix-method PWMscoreStartingAt reverseComplement,matrix-method unitScale
MIndex objects	ByPos_MIndex-class class:ByPos_MIndex class:MIndex coerce,MIndex,CompressedIRangesList-method elementNROWS,MIndex-method endIndex endIndex,ByPos_MIndex-method length,MIndex-method MIndex MIndex-class names,MIndex-method names<-,MIndex-method show,MIndex-method startIndex startIndex,ByPos_MIndex-method unlist,MIndex-method width0 width0,MIndex-method [[,ByPos_MIndex-method
Some miscellaneous stuff	misc N50
InDel objects	aligned alignedPattern alignedSubject compareStrings deletion errorSubstitutionMatrices indel insertion mismatchSummary mismatchTable moved_to_pwalign nedit nindel nucleotideSubstitutionMatrix pairwiseAlignment PairwiseAlignments PairwiseAlignmentsSingleSubject pid qualitySubstitutionMatrices stringDist unaligned writePairwiseAlignments
MultipleAlignment objects	AAMultipleAlignment AAMultipleAlignment-class alphabetFrequency,MultipleAlignment-method as.character,MultipleAlignment-method as.matrix,MultipleAlignment-method class:AAMultipleAlignment class:DNAMultipleAlignment class:MultipleAlignment class:RNAMultipleAlignment coerce,character,AAMultipleAlignment-method coerce,character,DNAMultipleAlignment-method coerce,character,RNAMultipleAlignment-method coerce,MultipleAlignment,AAStringSet-method coerce,MultipleAlignment,BStringSet-method coerce,MultipleAlignment,DNAStringSet-method coerce,MultipleAlignment,RNAStringSet-method colmask colmask,MultipleAlignment-method colmask<- colmask<-,MultipleAlignment,ANY-method colmask<-,MultipleAlignment,NULL-method consensusMatrix,MultipleAlignment-method consensusString,AAMultipleAlignment-method consensusString,DNAMultipleAlignment-method consensusString,MultipleAlignment-method consensusString,RNAMultipleAlignment-method consensusViews consensusViews,AAMultipleAlignment-method consensusViews,DNAMultipleAlignment-method consensusViews,MultipleAlignment-method consensusViews,RNAMultipleAlignment-method detail,MultipleAlignment-method dim,MultipleAlignment-method DNAMultipleAlignment DNAMultipleAlignment-class maskeddim maskeddim,MultipleAlignment-method maskedncol maskedncol,MultipleAlignment-method maskednrow maskednrow,MultipleAlignment-method maskedratio,MultipleAlignment-method maskGaps maskGaps,MultipleAlignment-method maskMotif,MultipleAlignment,ANY-method MultipleAlignment MultipleAlignment-class nchar,MultipleAlignment-method ncol,MultipleAlignment-method nrow,MultipleAlignment-method readAAMultipleAlignment readDNAMultipleAlignment readRNAMultipleAlignment RNAMultipleAlignment RNAMultipleAlignment-class rowmask rowmask,MultipleAlignment-method rowmask<- rowmask<-,MultipleAlignment,ANY-method rowmask<-,MultipleAlignment,NULL-method rownames,MultipleAlignment-method rownames<-,MultipleAlignment-method seqtype,MultipleAlignment-method show,MultipleAlignment-method unmasked,MultipleAlignment-method write.phylip
(Defunct) Needleman-Wunsch Global Alignment	needwunsQS
Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)	dinucleotideFrequency mkAllStrings nucleotideFrequencyAt nucleotideFrequencyAt,XStringSet-method nucleotideFrequencyAt,XStringViews-method oligonucleotideFrequency oligonucleotideFrequency,MaskedXString-method oligonucleotideFrequency,XString-method oligonucleotideFrequency,XStringSet-method oligonucleotideFrequency,XStringViews-method oligonucleotideTransitions trinucleotideFrequency
Pad and clip strings	padAndClip stackStrings
PDict objects	ACtree2 ACtree2-class as.list,MTB_PDict-method class:ACtree2 class:Expanded_TB_PDict class:MTB_PDict class:PDict class:PDict3Parts class:PreprocessedTB class:TB_PDict class:Twobit computeAllFlinks computeAllFlinks,ACtree2-method duplicated,PDict-method duplicated,PreprocessedTB-method Expanded_TB_PDict Expanded_TB_PDict-class hasAllFlinks hasAllFlinks,ACtree2-method head,PDict3Parts-method head,TB_PDict-method initialize,ACtree2-method initialize,PreprocessedTB-method initialize,Twobit-method length,PDict-method length,PDict3Parts-method length,PreprocessedTB-method MTB_PDict MTB_PDict-class names,PDict-method names<-,PDict-method nnodes nnodes,ACtree2-method patternFrequency patternFrequency,PDict-method PDict PDict,AsIs-method PDict,character-method PDict,DNAStringSet-method PDict,probetable-method PDict,XStringViews-method PDict-class PDict3Parts PDict3Parts-class PreprocessedTB PreprocessedTB-class show,ACtree2-method show,MTB_PDict-method show,TB_PDict-method show,Twobit-method tail,PDict3Parts-method tail,TB_PDict-method tb tb,PDict3Parts-method tb,PreprocessedTB-method tb,TB_PDict-method tb.width tb.width,PDict3Parts-method tb.width,PreprocessedTB-method tb.width,TB_PDict-method TB_PDict TB_PDict-class Twobit Twobit-class width,PDict-method width,PDict3Parts-method width,PreprocessedTB-method [[,PDict-method
Longest Common Prefix/Suffix/Substring searching functions	lcprefix lcprefix,character,character-method lcprefix,character,XString-method lcprefix,XString,character-method lcprefix,XString,XString-method lcsubstr lcsubstr,character,character-method lcsubstr,character,XString-method lcsubstr,XString,character-method lcsubstr,XString,XString-method lcsuffix lcsuffix,character,character-method lcsuffix,character,XString-method lcsuffix,XString,character-method lcsuffix,XString,XString-method pmatchPattern pmatchPattern,character-method pmatchPattern,XString-method pmatchPattern,XStringViews-method
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects	class:QualityScaledAAStringSet class:QualityScaledBStringSet class:QualityScaledDNAStringSet class:QualityScaledRNAStringSet class:QualityScaledXStringSet narrow,QualityScaledXStringSet-method parallel_slot_names,QualityScaledXStringSet-method quality quality,QualityScaledXStringSet-method QualityScaledAAStringSet QualityScaledAAStringSet-class QualityScaledBStringSet QualityScaledBStringSet-class QualityScaledDNAStringSet QualityScaledDNAStringSet-class QualityScaledRNAStringSet QualityScaledRNAStringSet-class QualityScaledXStringSet QualityScaledXStringSet-class readQualityScaledDNAStringSet reverse,QualityScaledXStringSet-method reverseComplement,QualityScaledDNAStringSet-method reverseComplement,QualityScaledRNAStringSet-method show,QualityScaledXStringSet-method windows,QualityScaledXStringSet-method writeQualityScaledXStringSet
Extract/replace arbitrary substrings from/in a string or set of strings.	extractAt extractAt,XString-method extractAt,XStringSet-method replaceAt replaceAt,XString-method replaceAt,XStringSet-method
Replacing letters in a sequence (or set of sequences) at some specified locations	.inplaceReplaceLetterAt replaceLetterAt replaceLetterAt,DNAString-method replaceLetterAt,DNAStringSet-method
Sequence reversing and complementing	complement complement,DNAString-method complement,DNAStringSet-method complement,MaskedDNAString-method complement,MaskedRNAString-method complement,RNAString-method complement,RNAStringSet-method complement,XStringViews-method reverse,MaskedXString-method reverseComplement reverseComplement,DNAString-method reverseComplement,DNAStringSet-method reverseComplement,MaskedDNAString-method reverseComplement,MaskedRNAString-method reverseComplement,RNAString-method reverseComplement,RNAStringSet-method reverseComplement,XStringViews-method
RNAString objects	class:RNAString RNAString RNAString-class RNA_ALPHABET RNA_BASES
seqinfo() method for DNAStringSet objects	seqinfo seqinfo,DNAStringSet-method seqinfo<-,DNAStringSet-method
Turning a DNA sequence into a vector of complex numbers	toComplex toComplex,DNAString-method
Translating DNA/RNA sequences	codons codons,DNAString-method codons,MaskedDNAString-method codons,MaskedRNAString-method codons,RNAString-method translate translate,DNAString-method translate,DNAStringSet-method translate,MaskedDNAString-method translate,MaskedRNAString-method translate,RNAString-method translate,RNAStringSet-method
Trim Flanking Patterns from Sequences	trimLRPatterns trimLRPatterns,character-method trimLRPatterns,XString-method trimLRPatterns,XStringSet-method
Concatenate sequences contained in XString, XStringSet and/or XStringViews objects	xscat
BString objects	!=,BString,character-method !=,character,BString-method !=,XString,XString-method ==,BString,character-method ==,character,BString-method ==,XString,XString-method alphabet alphabet,ANY-method as.character,XString-method as.vector,XString-method BString BString-class class:BString class:XString coerce,character,AAString-method coerce,character,BString-method coerce,character,DNAString-method coerce,character,RNAString-method coerce,character,XString-method coerce,XString,AAString-method coerce,XString,BString-method coerce,XString,DNAString-method coerce,XString,RNAString-method nchar,XString-method seqtype,AAString-method seqtype,BString-method seqtype,DNAString-method seqtype,RNAString-method seqtype<-,XString-method show,XString-method showAsCell,XString-method substr,XString-method substring,XString-method toString,XString-method updateObject,XString-method XString XString-class
XStringPartialMatches objects	class:XStringPartialMatches pattern pattern,XStringPartialMatches-method show,XStringPartialMatches-method subpatterns subpatterns,XStringPartialMatches-method XStringPartialMatches-class [,XStringPartialMatches-method
PhredQuality, SolexaQuality and IlluminaQuality objects	alphabet,XStringQuality-method as.matrix,XStringQuality-method as.vector,XStringQuality-method class:IlluminaQuality class:PhredQuality class:SolexaQuality class:XStringQuality coerce,BString,IlluminaQuality-method coerce,BString,PhredQuality-method coerce,BString,SolexaQuality-method coerce,BStringSet,IlluminaQuality-method coerce,BStringSet,PhredQuality-method coerce,BStringSet,SolexaQuality-method coerce,character,IlluminaQuality-method coerce,character,PhredQuality-method coerce,character,SolexaQuality-method coerce,integer,IlluminaQuality-method coerce,integer,PhredQuality-method coerce,integer,SolexaQuality-method coerce,IntegerList,IlluminaQuality-method coerce,IntegerList,PhredQuality-method coerce,IntegerList,SolexaQuality-method coerce,numeric,IlluminaQuality-method coerce,numeric,PhredQuality-method coerce,numeric,SolexaQuality-method coerce,NumericList,IlluminaQuality-method coerce,NumericList,PhredQuality-method coerce,NumericList,SolexaQuality-method coerce,XStringQuality,CompressedIntegerList-method coerce,XStringQuality,CompressedNumericList-method coerce,XStringQuality,IntegerList-method coerce,XStringQuality,matrix-method coerce,XStringQuality,NumericList-method encoding encoding,XStringQuality-method IlluminaQuality IlluminaQuality-class PhredQuality PhredQuality-class SolexaQuality SolexaQuality-class XStringQuality XStringQuality-class
XStringSet objects	AAStringSet AAStringSet-class as.character,XStringSet-method as.data.frame,XStringSet-method as.factor,XStringSet-method as.matrix,XStringSet-method as.vector,XStringSet-method BStringSet BStringSet-class class:AAStringSet class:BStringSet class:DNAStringSet class:RNAStringSet class:XStringSet coerce,ANY,AAStringSet-method coerce,ANY,BStringSet-method coerce,ANY,DNAStringSet-method coerce,ANY,RNAStringSet-method coerce,ANY,XStringSet-method DNAStringSet DNAStringSet-class narrow,character-method nchar,XStringSet-method RNAStringSet RNAStringSet-class seqtype,XStringSet-method seqtype<-,XStringSet-method show,XStringSet-method showAsCell,XStringSet-method subseq,character-method subseq<-,character-method subseq<-,XStringSet-method threebands,character-method toString,XStringSet-method unlist,XStringSet-method updateObject,XStringSet-method width,character-method windows,character-method XStringSet XStringSet-class
Comparing and ordering the elements in one or more XStringSet objects	anyNA,XStringSet-method is.na,XStringSet-method match,ANY,XStringSet-method match,XStringSet,ANY-method match,XStringSet,XStringSet-method pcompare,ANY,XStringSet-method pcompare,XStringSet,ANY-method pcompare,XStringSet,XStringSet-method XStringSet-comparison
Read/write an XStringSet object from/to a file	fasta.index fasta.seqlengths fastq.geometry fastq.seqlengths readAAStringSet readBStringSet readDNAStringSet readRNAStringSet saveXStringSet writeXStringSet XStringSet-io
XStringSetList objects	AAStringSetList AAStringSetList-class BStringSetList BStringSetList-class class:AAStringSetList class:BStringSetList class:DNAStringSetList class:RNAStringSetList class:XStringSetList coerce,List,AAStringSetList-method coerce,list,AAStringSetList-method coerce,List,BStringSetList-method coerce,list,BStringSetList-method coerce,List,DNAStringSetList-method coerce,list,DNAStringSetList-method coerce,List,RNAStringSetList-method coerce,list,RNAStringSetList-method coerce,List,XStringSetList-method coerce,list,XStringSetList-method DNAStringSetList DNAStringSetList-class nchar,XStringSetList-method relistToClass,XStringSet-method RNAStringSetList RNAStringSetList-class seqtype,XStringSetList-method seqtype<-,XStringSetList-method show,XStringSetList-method showAsCell,XStringSetList-method XStringSetList XStringSetList-class
The XStringViews class	!=,character,XStringViews-method !=,XString,XStringViews-method !=,XStringViews,character-method !=,XStringViews,XString-method !=,XStringViews,XStringViews-method ==,character,XStringViews-method ==,XString,XStringViews-method ==,XStringViews,character-method ==,XStringViews,XString-method ==,XStringViews,XStringViews-method as.character,XStringViews-method as.data.frame,XStringViews-method as.matrix,XStringViews-method class:XStringViews coerce,XStringSet,Views-method coerce,XStringSet,XStringViews-method coerce,XStringViews,AAStringSet-method coerce,XStringViews,BStringSet-method coerce,XStringViews,DNAStringSet-method coerce,XStringViews,RNAStringSet-method coerce,XStringViews,XStringSet-method nchar,XStringViews-method seqtype,XStringViews-method seqtype<-,XStringViews-method show,XStringViews-method toString,XStringViews-method Views,character-method Views,XString-method XStringViews XStringViews-class
An annotation data file for CHR1 in the yeastSEQ package	yeastSEQCHR1

Package: Biostrings 2.73.1

Biostrings: Efficient manipulation of biological strings

A short presentation of the basic classes defined in Biostrings 2

Biostrings Quick Overview

Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment

MultipleAlignment Objects

Pairwise Sequence Alignments

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Usage by other packages (reverse dependencies)