Package: Biostrings 2.75.3

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'))

Peer review:

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

Datasets:
  • BLOSUM100 - Predefined scoring matrices
  • BLOSUM45 - Predefined scoring matrices
  • BLOSUM50 - Predefined scoring matrices
  • BLOSUM62 - Predefined scoring matrices
  • BLOSUM80 - Predefined scoring matrices
  • HNF4alpha - Known HNF4alpha binding sequences
  • PAM120 - Predefined scoring matrices
  • PAM250 - Predefined scoring matrices
  • PAM30 - Predefined scoring matrices
  • PAM40 - Predefined scoring matrices
  • PAM70 - Predefined scoring matrices
  • yeastSEQCHR1 - An annotation data file for CHR1 in the yeastSEQ package

On BioConductor:Biostrings-2.75.2(bioc 3.21)Biostrings-2.74.0(bioc 3.20)

sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package

17.85 score 58 stars 1.2k packages 8.6k scripts 99k downloads 220 mentions 241 exports 18 dependencies

Last updated 2 days agofrom:1169409d62. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 16 2024
R-4.5-win-x86_64WARNINGDec 16 2024
R-4.5-linux-x86_64WARNINGDec 16 2024
R-4.4-win-x86_64WARNINGDec 16 2024
R-4.4-mac-x86_64WARNINGDec 16 2024
R-4.4-mac-aarch64WARNINGDec 16 2024
R-4.3-win-x86_64WARNINGDec 16 2024
R-4.3-mac-x86_64WARNINGDec 16 2024
R-4.3-mac-aarch64WARNINGDec 16 2024

Exports:.inplaceReplaceLetterAt%in%AA_ALPHABETAA_PROTEINOGENICAA_STANDARDAAMultipleAlignmentAAStringAAStringSetAAStringSetListalignedalignedPatternalignedSubjectalphabetalphabetFrequencyAMINO_ACID_CODEas.data.frameas.listas.matrixBStringBStringSetBStringSetListchartrcodonscoercecollapsecolmaskcolmask<-compareStringscomplementcomputeAllFlinksconsensusMatrixconsensusStringconsensusViewscountPatterncountPDictcountPWMcoveragedeletiondetaildinucleotideFrequencydinucleotideFrequencyTestDNA_ALPHABETDNA_BASESDNAMultipleAlignmentDNAStringDNAStringSetDNAStringSetListduplicatedencodingendendIndexerrorSubstitutionMatricesextract_character_from_XString_by_positionsextract_character_from_XString_by_rangesextractAllMatchesextractAtfasta.indexfasta.seqlengthsfastq.geometryfastq.seqlengthsfindPalindromesgapsGENETIC_CODEGENETIC_CODE_TABLEget_seqtype_conversion_lookupgetGeneticCodegetSeqgregexpr2hasAllFlinkshasLetterAthasOnlyBaseLettersheadIlluminaQualityindelinitializeinjectHardMaskinsertionintersectis.unsortedisMatchingAtisMatchingEndingAtisMatchingStartingAtIUPAC_CODE_MAPlcprefixlcsubstrlcsuffixletterletterFrequencyletterFrequencyInSlidingViewlongestConsecutivemake_XString_from_stringmake_XStringSet_from_stringsmaskmaskeddimmaskedncolmaskednrowmaskedratiomaskedwidthmaskGapsmaskMotifmasksmasks<-matchmatchLRPatternsmatchPatternmatchPDictmatchProbePairmatchprobesmatchPWMmaxScoremaxWeightsmergeIUPACLettersminScoreminWeightsmismatchmismatchSummarymismatchTablemkAllStringsN50ncharneditneditAtneditEndingAtneditStartingAtneedwunsQSnindelnmatchnmismatchnnodesnucleotideFrequencyAtnucleotideSubstitutionMatrixoligonucleotideFrequencyoligonucleotideTransitionsorderpadAndClippairwiseAlignmentPairwiseAlignmentsPairwiseAlignmentsSingleSubjectpalindromeArmLengthpalindromeLeftArmpalindromeRightArmparallel_slot_namesparallelVectorNamespatternpatternFrequencypcomparePDictPhredQualitypidpmatchPatternprint.moved_to_pwalign_pkgPWMPWMscoreStartingAtqualityQualityScaledAAStringSetQualityScaledBStringSetQualityScaledDNAStringSetQualityScaledRNAStringSetqualitySubstitutionMatricesrankreadAAMultipleAlignmentreadAAStringSetreadBStringSetreadDNAMultipleAlignmentreadDNAStringSetreadQualityScaledDNAStringSetreadRNAMultipleAlignmentreadRNAStringSetrelistToClassreplaceAmbiguitiesreplaceAtreplaceLetterAtreversereverseComplementRNA_ALPHABETRNA_BASESRNA_GENETIC_CODERNAMultipleAlignmentRNAStringRNAStringSetRNAStringSetListrowmaskrowmask<-saveXStringSetseqinfoseqinfo<-seqtypeseqtype<-setdiffsetequalshowshowAsCellSolexaQualitysortstackStringsstartstartIndexstringDiststrsplitsubpatternssubseqsubseq<-substrsubstringsummarytailtbtb.widththreebandstoComplextoStringtranslatetrimLRPatternstrinucleotideFrequencytwoWayAlphabetFrequencyunalignedunionuniqueLettersunitScaleunmaskedunstrsplitupdateObjectvcountPatternvcountPDictViewsvmatchPatternvmatchPDictvwhichPDictwhich.isMatchingAtwhich.isMatchingEndingAtwhich.isMatchingStartingAtwhichPDictwidthwidth0windowswrite.phylipwritePairwiseAlignmentswriteQualityScaledXStringSetwriteXStringSetxscatxscodes

Dependencies:askpassBiocGenericscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc

A short presentation of the basic classes defined in Biostrings 2

Rendered fromBiostrings2Classes.Rnwusingutils::Sweaveon Dec 16 2024.

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

Biostrings Quick Overview

Rendered fromBiostringsQuickOverview.Rnwusingutils::Sweaveon Dec 16 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 Dec 16 2024.

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

MultipleAlignment Objects

Marc Carlson, Beryl Kanali

Rendered fromMultipleAlignments.Rmdusingknitr::rmarkdownon Dec 16 2024.

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

Pairwise Sequence Alignments

Rendered fromPairwiseAlignments.Rnwusingutils::Sweaveon Dec 16 2024.

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

Readme and manuals

Help Manual

Help pageTopics
AAString objectsAAString AAString-class AA_ALPHABET AA_PROTEINOGENIC AA_STANDARD class:AAString
The Single-Letter Amino Acid CodeAMINO_ACID_CODE
Replace letters in a sequence or set of sequenceschartr 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 contentdetail
Pearson's chi-squared Test and G-tests for String Position DependencedinucleotideFrequencyTest dinucleotideFrequencyTest,DNAStringSet-method dinucleotideFrequencyTest,RNAStringSet-method
DNAString objectsclass:DNAString DNAString DNAString-class DNA_ALPHABET DNA_BASES
Searching a sequence for palindromesfindPalindromes 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 variantsGENETIC_CODE GENETIC_CODE_TABLE getGeneticCode RNA_GENETIC_CODE
getSeqgetSeq
A replacement for R standard gregexpr functiongregexpr2
Known HNF4alpha binding sequencesHNF4alpha
Injecting a hard mask in a sequenceinjectHardMask injectHardMask,MaskedXString-method injectHardMask,XStringViews-method
The IUPAC Extended Genetic AlphabetIUPAC_CODE_MAP mergeIUPACLetters
Subsetting a stringletter 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 sequencesalphabetFrequency 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 functionshasLetterAt 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 objectsas.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 functioncoverage,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 sequencematchLRPatterns matchLRPatterns,MaskedXString-method matchLRPatterns,XString-method matchLRPatterns,XStringViews-method
String searching functionscountPattern 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 referencecountPDict 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 pairmatchProbePair 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 utilitiescountPWM 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 objectsByPos_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 stuffmisc N50
InDel objectsaligned alignedPattern alignedSubject compareStrings deletion errorSubstitutionMatrices indel insertion mismatchSummary mismatchTable moved_to_pwalign nedit nindel nucleotideSubstitutionMatrix pairwiseAlignment PairwiseAlignments PairwiseAlignmentsSingleSubject pattern pid qualitySubstitutionMatrices stringDist unaligned writePairwiseAlignments
MultipleAlignment objectsAAMultipleAlignment 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 AlignmentneedwunsQS
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 stringspadAndClip stackStrings
PDict objectsACtree2 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 functionslcprefix 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
Predefined scoring matricesBLOSUM100 BLOSUM45 BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 PAM30 PAM40 PAM70 predefined_scoring_matrices print.moved_to_pwalign_pkg
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objectsclass: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 complementingcomplement 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 objectsclass:RNAString RNAString RNAString-class RNA_ALPHABET RNA_BASES
seqinfo() method for DNAStringSet objectsseqinfo seqinfo,DNAStringSet-method seqinfo<-,DNAStringSet-method
Turning a DNA sequence into a vector of complex numberstoComplex toComplex,DNAString-method
Translating DNA/RNA sequencescodons 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 SequencestrimLRPatterns trimLRPatterns,character-method trimLRPatterns,XString-method trimLRPatterns,XStringSet-method
Concatenate sequences contained in XString, XStringSet and/or XStringViews objectsxscat
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,AAString-method updateObject,XString-method XString XString-class
XStringPartialMatches objectsclass:XStringPartialMatches show,XStringPartialMatches-method subpatterns subpatterns,XStringPartialMatches-method XStringPartialMatches-class [,XStringPartialMatches-method
PhredQuality, SolexaQuality and IlluminaQuality objectsalphabet,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 objectsAAStringSet 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,AAStringSet-method updateObject,XStringSet-method width,character-method windows,character-method XStringSet XStringSet-class
Comparing and ordering the elements in one or more XStringSet objectsanyNA,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 filefasta.index fasta.seqlengths fastq.geometry fastq.seqlengths readAAStringSet readBStringSet readDNAStringSet readRNAStringSet saveXStringSet writeXStringSet XStringSet-io
XStringSetList objectsAAStringSetList 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 packageyeastSEQCHR1