Biostrings: String objects representing biological sequences, and matching algorithms

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

AuthorH. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Date of publicationNone
MaintainerH. Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version2.42.1

View on Bioconductor

Man pages

AAString-class: AAString objects

AlignedXStringSet-class: AlignedXStringSet and QualityAlignedXStringSet objects

align-utils: Utility functions related to sequence alignment

AMINO_ACID_CODE: The Single-Letter Amino Acid Code

Biostrings-internals: Biostrings internals

BOC_SubjectString-class: BOC\_SubjectString and BOC2\_SubjectString objects (DEFUNCT!)

chartr: Translating letters of a sequence

detail: Show (display) detailed object content

dinucleotideFrequencyTest: Pearson's chi-squared Test and G-tests for String Position...

DNAString-class: DNAString objects

findPalindromes: Searching a sequence for palindromes

GENETIC_CODE: The Standard Genetic Code and its known variants

getSeq: getSeq

gregexpr2: A replacement for R standard gregexpr function

HNF4alpha: Known HNF4alpha binding sequences

InDel-class: InDel objects

injectHardMask: Injecting a hard mask in a sequence

IUPAC_CODE_MAP: The IUPAC Extended Genetic Alphabet

letter: Subsetting a string

letterFrequency: Calculate the frequency of letters in a biological sequence,...

longestConsecutive: Obtain the length of the longest substring containing only...

lowlevel-matching: Low-level matching functions

MaskedXString-class: MaskedXString objects

maskMotif: Masking by content (or by position)

matchLRPatterns: Find paired matches in a sequence

matchPattern: String searching functions

matchPDict-exact: Matching a dictionary of patterns against a reference

matchPDict-inexact: Inexact matching with matchPDict()/countPDict()/whichPDict()

matchProbePair: Find "theoretical amplicons" mapped to a probe pair

matchprobes: A function to match a query sequence to the sequences of a...

matchPWM: PWM creating, matching, and related utilities

match-utils: Utility functions operating on the matches returned by a...

MIndex-class: MIndex objects

misc: Some miscellaneous stuff

MultipleAlignment-class: MultipleAlignment objects

needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment

nucleotideFrequency: Calculate the frequency of oligonucleotides in a DNA or RNA...

padAndClip: Pad and clip strings

pairwiseAlignment: Optimal Pairwise Alignment

PairwiseAlignments-class: PairwiseAlignments, PairwiseAlignmentsSingleSubject, and...

PairwiseAlignments-io: Write a PairwiseAlignments object to a file

PDict-class: PDict objects

phiX174Phage: Versions of bacteriophage phiX174 complete genome and sample...

pid: Percent Sequence Identity

pmatchPattern: Longest Common Prefix/Suffix/Substring searching functions

QualityScaledXStringSet-class: QualityScaledBStringSet, QualityScaledDNAStringSet,...

replaceAt: Extract/replace arbitrary substrings from/in a string or set...

replaceLetterAt: Replacing letters in a sequence (or set of sequences) at some...

reverseComplement: Sequence reversing and complementing

RNAString-class: RNAString objects

stringDist: String Distance/Alignment Score Matrix

substitution_matrices: Scoring matrices

toComplex: Turning a DNA sequence into a vector of complex numbers

translate: Translating DNA/RNA sequences

trimLRPatterns: Trim Flanking Patterns from Sequences

xscat: Concatenate sequences contained in XString, XStringSet and/or...

XString-class: BString objects

XStringPartialMatches-class: XStringPartialMatches objects

XStringQuality-class: PhredQuality, SolexaQuality and IlluminaQuality objects

XStringSet-class: XStringSet objects

XStringSet-comparison: Comparing and ordering the elements in one or more XStringSet...

XStringSet-io: Read/write an XStringSet object from/to a file

XStringSetList-class: XStringSetList objects

XStringViews-class: The XStringViews class

yeastSEQCHR1: An annotation data file for CHR1 in the yeastSEQ package

Functions

AA_ALPHABET Man page
AAMultipleAlignment Man page
AAMultipleAlignment-class Man page
AA_PROTEINOGENIC Man page
AA_STANDARD Man page
AAString Man page
AAString-class Man page
AAStringSet Man page
AAStringSet-class Man page
AAStringSetList Man page
AAStringSetList-class Man page
ACtree2 Man page
ACtree2-class Man page
aligned Man page
aligned,AlignedXStringSet0-method Man page
aligned,PairwiseAlignmentsSingleSubject-method Man page
AlignedXStringSet Man page
AlignedXStringSet0 Man page
AlignedXStringSet0-class Man page
[<-,AlignedXStringSet0-method Man page
[,AlignedXStringSet0-method Man page
AlignedXStringSet-class Man page
align-utils Man page
alphabet Man page
alphabet,ANY-method Man page
alphabetFrequency Man page
alphabetFrequency,AAString-method Man page
alphabetFrequency,AAStringSet-method Man page
alphabetFrequency,DNAString-method Man page
alphabetFrequency,DNAStringSet-method Man page
alphabetFrequency,MaskedXString-method Man page
alphabetFrequency,MultipleAlignment-method Man page
alphabetFrequency,RNAString-method Man page
alphabetFrequency,RNAStringSet-method Man page
alphabetFrequency,XString-method Man page
alphabetFrequency,XStringSet-method Man page
alphabetFrequency,XStringViews-method Man page
alphabet,XStringQuality-method Man page
AMINO_ACID_CODE Man page
anyNA,XStringSet-method Man page
append,QualityScaledXStringSet,QualityScaledXStringSet-method Man page
as.character,AlignedXStringSet0-method Man page
as.character,MaskedXString-method Man page
as.character,MultipleAlignment-method Man page
as.character,PairwiseAlignmentsSingleSubject-method Man page
as.character,XString-method Man page
as.character,XStringSet-method Man page
as.character,XStringViews-method Man page
as.data.frame,XStringSet-method Man page
as.data.frame,XStringViews-method Man page
as.factor,XStringSet-method Man page
as.list,MTB_PDict-method Man page
as.list,SparseList-method Man page
as.matrix,MultipleAlignment-method Man page
as.matrix,PairwiseAlignmentsSingleSubject-method Man page
as.matrix,XStringQuality-method Man page
as.matrix,XStringSet-method Man page
as.matrix,XStringViews-method Man page
as.vector,XString-method Man page
as.vector,XStringQuality-method Man page
as.vector,XStringSet-method Man page
BLOSUM100 Man page
BLOSUM45 Man page
BLOSUM50 Man page
BLOSUM62 Man page
BLOSUM80 Man page
BOC2_SubjectString Man page
BOC2_SubjectString-class Man page
BOC_SubjectString Man page
BOC_SubjectString-class Man page
BString Man page
==,BString,character-method Man page
!=,BString,character-method Man page
BString-class Man page
BStringSet Man page
BStringSet-class Man page
BStringSetList Man page
BStringSetList-class Man page
ByPos_MIndex-class Man page
[[,ByPos_MIndex-method Man page
==,character,BString-method Man page
!=,character,BString-method Man page
==,character,XStringViews-method Man page
!=,character,XStringViews-method Man page
chartr,ANY,ANY,MaskedXString-method Man page
chartr,ANY,ANY,XString-method Man page
chartr,ANY,ANY,XStringSet-method Man page
chartr,ANY,ANY,XStringViews-method Man page
class:AAMultipleAlignment Man page
class:AAString Man page
class:AAStringSet Man page
class:AAStringSetList Man page
class:ACtree2 Man page
class:AlignedXStringSet Man page
class:AlignedXStringSet0 Man page
class:BOC2_SubjectString Man page
class:BOC_SubjectString Man page
class:BString Man page
class:BStringSet Man page
class:BStringSetList Man page
class:ByPos_MIndex Man page
class:DNAMultipleAlignment Man page
class:DNAString Man page
class:DNAStringSet Man page
class:DNAStringSetList Man page
class:Expanded_TB_PDict Man page
class:IlluminaQuality Man page
class:InDel Man page
class:MaskedAAString Man page
class:MaskedBString Man page
class:MaskedDNAString Man page
class:MaskedRNAString Man page
class:MaskedXString Man page
class:MIndex Man page
class:MTB_PDict Man page
class:MultipleAlignment Man page
class:PairwiseAlignments Man page
class:PairwiseAlignmentsSingleSubject Man page
class:PairwiseAlignmentsSingleSubjectSummary Man page
class:PDict Man page
class:PDict3Parts Man page
class:PhredQuality Man page
class:PreprocessedTB Man page
class:QualityAlignedXStringSet Man page
class:QualityScaledAAStringSet Man page
class:QualityScaledBStringSet Man page
class:QualityScaledDNAStringSet Man page
class:QualityScaledRNAStringSet Man page
class:QualityScaledXStringSet Man page
class:RNAMultipleAlignment Man page
class:RNAString Man page
class:RNAStringSet Man page
class:RNAStringSetList Man page
class:SolexaQuality Man page
class:SparseList Man page
class:TB_PDict Man page
class:Twobit Man page
class:XString Man page
class:XStringCodec Man page
class:XStringPartialMatches Man page
class:XStringQuality Man page
class:XStringSet Man page
class:XStringSetList Man page
class:XStringViews Man page
codons Man page
codons,DNAString-method Man page
codons,MaskedDNAString-method Man page
codons,MaskedRNAString-method Man page
codons,RNAString-method Man page
coerce,AAString,MaskedAAString-method Man page
coerce,ANY,AAStringSet-method Man page
coerce,ANY,BStringSet-method Man page
coerce,ANY,DNAStringSet-method Man page
coerce,ANY,RNAStringSet-method Man page
coerce,ANY,XStringSet-method Man page
coerce,BString,IlluminaQuality-method Man page
coerce,BString,MaskedBString-method Man page
coerce,BString,PhredQuality-method Man page
coerce,BStringSet,IlluminaQuality-method Man page
coerce,BStringSet,PhredQuality-method Man page
coerce,BStringSet,SolexaQuality-method Man page
coerce,BString,SolexaQuality-method Man page
coerce,character,AAMultipleAlignment-method Man page
coerce,character,AAString-method Man page
coerce,character,BString-method Man page
coerce,character,DNAMultipleAlignment-method Man page
coerce,character,DNAString-method Man page
coerce,character,IlluminaQuality-method Man page
coerce,character,PhredQuality-method Man page
coerce,character,RNAMultipleAlignment-method Man page
coerce,character,RNAString-method Man page
coerce,character,SolexaQuality-method Man page
coerce,character,XString-method Man page
coerce,DNAString,MaskedDNAString-method Man page
coerce,integer,IlluminaQuality-method Man page
coerce,IntegerList,IlluminaQuality-method Man page
coerce,IntegerList,PhredQuality-method Man page
coerce,IntegerList,SolexaQuality-method Man page
coerce,integer,PhredQuality-method Man page
coerce,integer,SolexaQuality-method Man page
coerce,MaskedAAString,AAString-method Man page
coerce,MaskedBString,BString-method Man page
coerce,MaskedDNAString,DNAString-method Man page
coerce,MaskedRNAString,RNAString-method Man page
coerce,MaskedXString,MaskCollection-method Man page
coerce,MaskedXString,MaskedAAString-method Man page
coerce,MaskedXString,MaskedBString-method Man page
coerce,MaskedXString,MaskedDNAString-method Man page
coerce,MaskedXString,MaskedRNAString-method Man page
coerce,MaskedXString,NormalIRanges-method Man page
coerce,MaskedXString,Views-method Man page
coerce,MaskedXString,XStringViews-method Man page
coerce,MIndex,CompressedIRangesList-method Man page
coerce,MultipleAlignment,AAStringSet-method Man page
coerce,MultipleAlignment,BStringSet-method Man page
coerce,MultipleAlignment,DNAStringSet-method Man page
coerce,MultipleAlignment,RNAStringSet-method Man page
coerce,numeric,IlluminaQuality-method Man page
coerce,NumericList,IlluminaQuality-method Man page
coerce,NumericList,PhredQuality-method Man page
coerce,NumericList,SolexaQuality-method Man page
coerce,numeric,PhredQuality-method Man page
coerce,numeric,SolexaQuality-method Man page
coerce,RNAString,MaskedRNAString-method Man page
coerce,XString,AAString-method Man page
coerce,XString,BString-method Man page
coerce,XString,DNAString-method Man page
coerce,XStringQuality,IntegerList-method Man page
coerce,XStringQuality,matrix-method Man page
coerce,XStringQuality,NumericList-method Man page
coerce,XString,RNAString-method Man page
coerce,XStringSet,Views-method Man page
coerce,XStringSet,XStringViews-method Man page
coerce,XStringViews,AAStringSet-method Man page
coerce,XStringViews,BStringSet-method Man page
coerce,XStringViews,DNAStringSet-method Man page
coerce,XStringViews,RNAStringSet-method Man page
coerce,XStringViews,XStringSet-method Man page
collapse,MaskedXString-method Man page
colmask Man page
colmask<- Man page
colmask<-,MultipleAlignment,ANY-method Man page
colmask,MultipleAlignment-method Man page
colmask<-,MultipleAlignment,NormalIRanges-method Man page
colmask<-,MultipleAlignment,NULL-method Man page
compareStrings Man page
compareStrings,AlignedXStringSet0,AlignedXStringSet0-method Man page
compareStrings,character,character-method Man page
compareStrings,PairwiseAlignments,missing-method Man page
compareStrings,XStringSet,XStringSet-method Man page
compareStrings,XString,XString-method Man page
complement Man page
complement,DNAString-method Man page
complement,DNAStringSet-method Man page
complement,MaskedDNAString-method Man page
complement,MaskedRNAString-method Man page
complement,RNAString-method Man page
complement,RNAStringSet-method Man page
complement,XStringViews-method Man page
computeAllFlinks Man page
computeAllFlinks,ACtree2-method Man page
consensusMatrix Man page
consensusMatrix,character-method Man page
consensusMatrix,matrix-method Man page
consensusMatrix,MultipleAlignment-method Man page
consensusMatrix,PairwiseAlignmentsSingleSubject-method Man page
consensusMatrix,XStringSet-method Man page
consensusMatrix,XStringViews-method Man page
consensusString Man page
consensusString,AAMultipleAlignment-method Man page
consensusString,ANY-method Man page
consensusString,BStringSet-method Man page
consensusString,DNAMultipleAlignment-method Man page
consensusString,DNAStringSet-method Man page
consensusString,matrix-method Man page
consensusString,MultipleAlignment-method Man page
consensusString,RNAMultipleAlignment-method Man page
consensusString,RNAStringSet-method Man page
consensusString,XStringViews-method Man page
consensusViews Man page
consensusViews,AAMultipleAlignment-method Man page
consensusViews,DNAMultipleAlignment-method Man page
consensusViews,MultipleAlignment-method Man page
consensusViews,RNAMultipleAlignment-method Man page
countPattern Man page
countPattern,BOC2_SubjectString-method Man page
countPattern,character-method Man page
countPattern,MaskedXString-method Man page
countPattern,XString-method Man page
countPattern,XStringSet-method Man page
countPattern,XStringViews-method Man page
countPDict Man page
countPDict,MaskedXString-method Man page
countPDict,XString-method Man page
countPDict,XStringSet-method Man page
countPDict,XStringViews-method Man page
countPWM Man page
countPWM,character-method Man page
countPWM,DNAString-method Man page
countPWM,MaskedDNAString-method Man page
countPWM,XStringViews-method Man page
coverage,AlignedXStringSet0-method Man page
coverage,MaskedXString-method Man page
coverage,MIndex-method Man page
coverage,PairwiseAlignmentsSingleSubject-method Man page
coverage,PairwiseAlignmentsSingleSubjectSummary-method Man page
deletion Man page
deletion,InDel-method Man page
deletion,PairwiseAlignments-method Man page
detail Man page
detail,MultipleAlignment-method Man page
dim,MultipleAlignment-method Man page
dinucleotideFrequency Man page
dinucleotideFrequencyTest Man page
dinucleotideFrequencyTest,DNAStringSet-method Man page
dinucleotideFrequencyTest,RNAStringSet-method Man page
DNA_ALPHABET Man page
DNA_BASES Man page
DNAMultipleAlignment Man page
DNAMultipleAlignment-class Man page
DNAString Man page
DNAString-class Man page
DNAStringSet Man page
DNAStringSet-class Man page
DNAStringSetList Man page
DNAStringSetList-class Man page
duplicated,PDict-method Man page
duplicated,PreprocessedTB-method Man page
elementNROWS,MIndex-method Man page
encoding Man page
encoding,XStringQuality-method Man page
end,AlignedXStringSet0-method Man page
endIndex Man page
endIndex,ByPos_MIndex-method Man page
errorSubstitutionMatrices Man page
Expanded_TB_PDict Man page
Expanded_TB_PDict-class Man page
extractAllMatches Man page
extractAt Man page
extractAt,XString-method Man page
extractAt,XStringSet-method Man page
fasta.index Man page
fasta.seqlengths Man page
fastq.geometry Man page
findPalindromes Man page
findPalindromes,DNAString-method Man page
findPalindromes,MaskedXString-method Man page
findPalindromes,RNAString-method Man page
findPalindromes,XString-method Man page
findPalindromes,XStringViews-method Man page
gaps,MaskedXString-method Man page
GENETIC_CODE Man page
GENETIC_CODE_TABLE Man page
getGeneticCode Man page
getSeq Man page
get_seqtype_conversion_lookup Man page
gregexpr2 Man page
hasAllFlinks Man page
hasAllFlinks,ACtree2-method Man page
hasLetterAt Man page
hasOnlyBaseLetters Man page
hasOnlyBaseLetters,DNAString-method Man page
hasOnlyBaseLetters,DNAStringSet-method Man page
hasOnlyBaseLetters,MaskedXString-method Man page
hasOnlyBaseLetters,RNAString-method Man page
hasOnlyBaseLetters,RNAStringSet-method Man page
hasOnlyBaseLetters,XStringViews-method Man page
head,PDict3Parts-method Man page
head,TB_PDict-method Man page
HNF4alpha Man page
IlluminaQuality Man page
IlluminaQuality-class Man page
indel Man page
InDel Man page
indel,AlignedXStringSet0-method Man page
InDel-class Man page
indel,PairwiseAlignments-method Man page
initialize,ACtree2-method Man page
initialize,BOC2_SubjectString-method Man page
initialize,BOC_SubjectString-method Man page
initialize,PreprocessedTB-method Man page
initialize,Twobit-method Man page
initialize,XStringCodec-method Man page
injectHardMask Man page
injectHardMask,MaskedXString-method Man page
injectHardMask,XStringViews-method Man page
.inplaceReplaceLetterAt Man page
insertion Man page
insertion,InDel-method Man page
insertion,PairwiseAlignments-method Man page
isMatchingAt Man page
isMatchingEndingAt Man page
isMatchingEndingAt,character-method Man page
isMatchingEndingAt,XString-method Man page
isMatchingEndingAt,XStringSet-method Man page
isMatchingStartingAt Man page
isMatchingStartingAt,character-method Man page
isMatchingStartingAt,XString-method Man page
isMatchingStartingAt,XStringSet-method Man page
is.na,XStringSet-method Man page
IUPAC_CODE_MAP Man page
lcprefix Man page
lcprefix,character,character-method Man page
lcprefix,character,XString-method Man page
lcprefix,XString,character-method Man page
lcprefix,XString,XString-method Man page
lcsubstr Man page
lcsubstr,character,character-method Man page
lcsubstr,character,XString-method Man page
lcsubstr,XString,character-method Man page
lcsubstr,XString,XString-method Man page
lcsuffix Man page
lcsuffix,character,character-method Man page
lcsuffix,character,XString-method Man page
lcsuffix,XString,character-method Man page
lcsuffix,XString,XString-method Man page
length,AlignedXStringSet0-method Man page
length,MaskedXString-method Man page
length,MIndex-method Man page
length,PairwiseAlignments-method Man page
length,PairwiseAlignmentsSingleSubjectSummary-method Man page
length,PDict3Parts-method Man page
length,PDict-method Man page
length,PreprocessedTB-method Man page
length,SparseList-method Man page
letter Man page
letter,character-method Man page
letterFrequency Man page
letterFrequencyInSlidingView Man page
letterFrequencyInSlidingView,MaskedXString-method Man page
letterFrequencyInSlidingView,XString-method Man page
letterFrequencyInSlidingView,XStringSet-method Man page
letterFrequencyInSlidingView,XStringViews-method Man page
letterFrequency,MaskedXString-method Man page
letterFrequency,XString-method Man page
letterFrequency,XStringSet-method Man page
letterFrequency,XStringViews-method Man page
letter,MaskedXString-method Man page
letter,XString-method Man page
letter,XStringViews-method Man page
longestConsecutive Man page
lowlevel-matching Man page
ls,SparseList-method Man page
mask Man page
MaskedAAString Man page
MaskedAAString-class Man page
MaskedBString Man page
MaskedBString-class Man page
maskeddim Man page
maskeddim,MultipleAlignment-method Man page
MaskedDNAString Man page
MaskedDNAString-class Man page
maskedncol Man page
maskedncol,MultipleAlignment-method Man page
maskednrow Man page
maskednrow,MultipleAlignment-method Man page
maskedratio,MaskedXString-method Man page
maskedratio,MultipleAlignment-method Man page
MaskedRNAString Man page
MaskedRNAString-class Man page
maskedwidth,MaskedXString-method Man page
MaskedXString Man page
MaskedXString-class Man page
maskGaps Man page
maskGaps,MultipleAlignment-method Man page
maskMotif Man page
maskMotif,MaskedXString,character-method Man page
maskMotif,MaskedXString,XString-method Man page
maskMotif,MultipleAlignment,ANY-method Man page
maskMotif,XString,ANY-method Man page
masks Man page
masks<- Man page
masks<-,MaskedXString,MaskCollection-method Man page
masks,MaskedXString-method Man page
masks<-,MaskedXString,NULL-method Man page
masks<-,XString,ANY-method Man page
masks,XString-method Man page
masks<-,XString,NULL-method Man page
match,ANY,XStringSet-method Man page
matchLRPatterns Man page
matchLRPatterns,MaskedXString-method Man page
matchLRPatterns,XString-method Man page
matchLRPatterns,XStringViews-method Man page
matchPattern Man page
matchPattern,BOC2_SubjectString-method Man page
matchPattern,BOC_SubjectString-method Man page
matchPattern,character-method Man page
matchPattern,MaskedXString-method Man page
matchPattern,XString-method Man page
matchPattern,XStringSet-method Man page
matchPattern,XStringViews-method Man page
matchPDict Man page
matchPDict-exact Man page
matchPDict-inexact Man page
matchPDict,MaskedXString-method Man page
matchPDict,XString-method Man page
matchPDict,XStringSet-method Man page
matchPDict,XStringViews-method Man page
matchProbePair Man page
matchProbePair,DNAString-method Man page
matchProbePair,MaskedDNAString-method Man page
matchProbePair,XStringViews-method Man page
matchprobes Man page
matchPWM Man page
matchPWM,character-method Man page
matchPWM,DNAString-method Man page
matchPWM,MaskedDNAString-method Man page
matchPWM,XStringViews-method Man page
match-utils Man page
match,XStringSet,ANY-method Man page
match,XStringSet,XStringSet-method Man page
maxScore Man page
maxScore,ANY-method Man page
maxWeights Man page
maxWeights,matrix-method Man page
mergeIUPACLetters Man page
MIndex Man page
MIndex-class Man page
minScore Man page
minScore,ANY-method Man page
minWeights Man page
minWeights,matrix-method Man page
misc Man page
mismatch Man page
mismatch,AlignedXStringSet0,missing-method Man page
mismatch,ANY,XStringViews-method Man page
mismatchSummary Man page
mismatchSummary,AlignedXStringSet0-method Man page
mismatchSummary,PairwiseAlignmentsSingleSubject-method Man page
mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method Man page
mismatchSummary,QualityAlignedXStringSet-method Man page
mismatchTable Man page
mismatchTable,AlignedXStringSet0-method Man page
mismatchTable,PairwiseAlignments-method Man page
mismatchTable,QualityAlignedXStringSet-method Man page
mkAllStrings Man page
MTB_PDict Man page
MTB_PDict-class Man page
MultipleAlignment Man page
MultipleAlignment-class Man page
N50 Man page
names<-,MIndex-method Man page
names,MIndex-method Man page
names<-,PDict-method Man page
names,PDict-method Man page
narrow,character-method Man page
narrow,QualityScaledXStringSet-method Man page
nchar,AlignedXStringSet0-method Man page
nchar,MaskedXString-method Man page
nchar,MultipleAlignment-method Man page
nchar,PairwiseAlignments-method Man page
nchar,PairwiseAlignmentsSingleSubjectSummary-method Man page
nchar,XString-method Man page
nchar,XStringSetList-method Man page
nchar,XStringSet-method Man page
nchar,XStringViews-method Man page
ncol,MultipleAlignment-method Man page
nedit Man page
neditAt Man page
neditEndingAt Man page
neditEndingAt,character-method Man page
neditEndingAt,XString-method Man page
neditEndingAt,XStringSet-method Man page
nedit,PairwiseAlignments-method Man page
nedit,PairwiseAlignmentsSingleSubjectSummary-method Man page
neditStartingAt Man page
neditStartingAt,character-method Man page
neditStartingAt,XString-method Man page
neditStartingAt,XStringSet-method Man page
needwunsQS Man page
needwunsQS,character,character-method Man page
needwunsQS,character,XString-method Man page
needwunsQS,XString,character-method Man page
needwunsQS,XString,XString-method Man page
nindel Man page
nindel,AlignedXStringSet0-method Man page
nindel,PairwiseAlignments-method Man page
nindel,PairwiseAlignmentsSingleSubjectSummary-method Man page
nmatch Man page
nmatch,ANY,XStringViews-method Man page
nmatch,PairwiseAlignments,missing-method Man page
nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method Man page
nmismatch Man page
nmismatch,AlignedXStringSet0,missing-method Man page
nmismatch,ANY,XStringViews-method Man page
nmismatch,PairwiseAlignments,missing-method Man page
nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method Man page
nnodes Man page
nnodes,ACtree2-method Man page
nrow,MultipleAlignment-method Man page
nucleotideFrequencyAt Man page
nucleotideFrequencyAt,XStringSet-method Man page
nucleotideFrequencyAt,XStringViews-method Man page
nucleotideSubstitutionMatrix Man page
oligonucleotideFrequency Man page
oligonucleotideFrequency Man page
oligonucleotideFrequency,MaskedXString-method Man page
oligonucleotideFrequency,XString-method Man page
oligonucleotideFrequency,XStringSet-method Man page
oligonucleotideFrequency,XStringViews-method Man page
oligonucleotideTransitions Man page
padAndClip Man page
pairwiseAlignment Man page
pairwiseAlignment,ANY,ANY-method Man page
pairwiseAlignment,ANY,QualityScaledXStringSet-method Man page
pairwiseAlignment,QualityScaledXStringSet,ANY-method Man page
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSe Man page
PairwiseAlignments Man page
PairwiseAlignments,character,character-method Man page
PairwiseAlignments,character,missing-method Man page
PairwiseAlignments-class Man page
PairwiseAlignments-io Man page
[<-,PairwiseAlignments-method Man page
[,PairwiseAlignments-method Man page
PairwiseAlignmentsSingleSubject Man page
PairwiseAlignmentsSingleSubject,character,character-method Man page
PairwiseAlignmentsSingleSubject,character,missing-method Man page
PairwiseAlignmentsSingleSubject-class Man page
PairwiseAlignmentsSingleSubjectSummary Man page
PairwiseAlignmentsSingleSubjectSummary-class Man page
PairwiseAlignmentsSingleSubject,XStringSet,missing-method Man page
PairwiseAlignmentsSingleSubject,XString,XString-method Man page
PairwiseAlignments,XStringSet,missing-method Man page
PairwiseAlignments,XString,XString-method Man page
palindromeArmLength Man page
palindromeArmLength,DNAString-method Man page
palindromeArmLength,RNAString-method Man page
palindromeArmLength,XString-method Man page
palindromeArmLength,XStringViews-method Man page
palindromeLeftArm Man page
palindromeLeftArm,XString-method Man page
palindromeLeftArm,XStringViews-method Man page
palindromeRightArm Man page
palindromeRightArm,XString-method Man page
palindromeRightArm,XStringViews-method Man page
PAM120 Man page
PAM250 Man page
PAM30 Man page
PAM40 Man page
PAM70 Man page
pattern Man page
patternFrequency Man page
patternFrequency,PDict-method Man page
pattern,PairwiseAlignments-method Man page
pattern,XStringPartialMatches-method Man page
pcompare,ANY,XStringSet-method Man page
pcompare,XStringSet,ANY-method Man page
pcompare,XStringSet,XStringSet-method Man page
PDict Man page
PDict3Parts Man page
PDict3Parts-class Man page
PDict,AsIs-method Man page
PDict,character-method Man page
PDict-class Man page
PDict,DNAStringSet-method Man page
[[,PDict-method Man page
PDict,probetable-method Man page
PDict,XStringViews-method Man page
phiX174Phage Man page
PhredQuality Man page
PhredQuality-class Man page
pid Man page
pid,PairwiseAlignments-method Man page
pmatchPattern Man page
pmatchPattern,character-method Man page
pmatchPattern,XString-method Man page
pmatchPattern,XStringViews-method Man page
PreprocessedTB Man page
PreprocessedTB-class Man page
print.needwunsQS Man page
PWM Man page
PWM,character-method Man page
PWM,DNAStringSet-method Man page
PWM,matrix-method Man page
PWMscoreStartingAt Man page
quality Man page
QualityAlignedXStringSet Man page
QualityAlignedXStringSet-class Man page
quality,QualityScaledXStringSet-method Man page
QualityScaledAAStringSet Man page
QualityScaledAAStringSet-class Man page
QualityScaledBStringSet Man page
QualityScaledBStringSet-class Man page
QualityScaledDNAStringSet Man page
QualityScaledDNAStringSet-class Man page
QualityScaledRNAStringSet Man page
QualityScaledRNAStringSet-class Man page
QualityScaledXStringSet Man page
QualityScaledXStringSet-class Man page
[,QualityScaledXStringSet-method Man page
qualitySubstitutionMatrices Man page
quPhiX174 Man page
readAAMultipleAlignment Man page
readAAStringSet Man page
readBStringSet Man page
readDNAMultipleAlignment Man page
readDNAStringSet Man page
readRNAMultipleAlignment Man page
readRNAStringSet Man page
rep,AlignedXStringSet0-method Man page
replaceAt Man page
replaceAt,XString-method Man page
replaceAt,XStringSet-method Man page
replaceLetterAt Man page
replaceLetterAt,DNAString-method Man page
replaceLetterAt,DNAStringSet-method Man page
rep,PairwiseAlignments-method Man page
reverseComplement Man page
reverseComplement,DNAString-method Man page
reverseComplement,DNAStringSet-method Man page
reverseComplement,MaskedDNAString-method Man page
reverseComplement,MaskedRNAString-method Man page
reverseComplement,matrix-method Man page
reverseComplement,RNAString-method Man page
reverseComplement,RNAStringSet-method Man page
reverseComplement,XStringViews-method Man page
reverse,MaskedXString-method Man page
RNA_ALPHABET Man page
RNA_BASES Man page
RNA_GENETIC_CODE Man page
RNAMultipleAlignment Man page
RNAMultipleAlignment-class Man page
RNAString Man page
RNAString-class Man page
RNAStringSet Man page
RNAStringSet-class Man page
RNAStringSetList Man page
RNAStringSetList-class Man page
rowmask Man page
rowmask<- Man page
rowmask<-,MultipleAlignment,ANY-method Man page
rowmask,MultipleAlignment-method Man page
rowmask<-,MultipleAlignment,NormalIRanges-method Man page
rowmask<-,MultipleAlignment,NULL-method Man page
rownames<-,MultipleAlignment-method Man page
rownames,MultipleAlignment-method Man page
saveXStringSet Man page
score,PairwiseAlignments-method Man page
score,PairwiseAlignmentsSingleSubjectSummary-method Man page
seqtype Man page
seqtype<- Man page
seqtype,AAString-method Man page
seqtype,AlignedXStringSet0-method Man page
seqtype,BString-method Man page
seqtype,DNAString-method Man page
seqtype<-,MaskedXString-method Man page
seqtype,MaskedXString-method Man page
seqtype,MultipleAlignment-method Man page
seqtype,PairwiseAlignments-method Man page
seqtype,RNAString-method Man page
seqtype<-,XString-method Man page
seqtype<-,XStringSetList-method Man page
seqtype,XStringSetList-method Man page
seqtype<-,XStringSet-method Man page
seqtype,XStringSet-method Man page
seqtype<-,XStringViews-method Man page
seqtype,XStringViews-method Man page
show,ACtree2-method Man page
show,AlignedXStringSet0-method Man page
showAsCell,XString-method Man page
showAsCell,XStringSet-method Man page
show,MaskedXString-method Man page
show,MIndex-method Man page
show,MTB_PDict-method Man page
show,MultipleAlignment-method Man page
show,PairwiseAlignments-method Man page
show,PairwiseAlignmentsSingleSubjectSummary-method Man page
show,QualityScaledXStringSet-method Man page
show,TB_PDict-method Man page
show,Twobit-method Man page
show,XString-method Man page
show,XStringPartialMatches-method Man page
show,XStringSetList-method Man page
show,XStringSet-method Man page
show,XStringViews-method Man page
SolexaQuality Man page
SolexaQuality-class Man page
SparseList Man page
SparseList-class Man page
[[,SparseList-method Man page
srPhiX174 Man page
stackStrings Man page
start,AlignedXStringSet0-method Man page
startIndex Man page
startIndex,ByPos_MIndex-method Man page
stringDist Man page
stringDist,character-method Man page
stringDist,QualityScaledXStringSet-method Man page
stringDist,XStringSet-method Man page
subject,PairwiseAlignments-method Man page
subpatterns Man page
subpatterns,XStringPartialMatches-method Man page
subseq<-,character-method Man page
subseq,character-method Man page
subseq,MaskedXString-method Man page
subseq<-,XStringSet-method Man page
substitution.matrices Man page
substring,XString-method Man page
substr,XString-method Man page
summary,PairwiseAlignmentsSingleSubject-method Man page
tail,PDict3Parts-method Man page
tail,TB_PDict-method Man page
tb Man page
TB_PDict Man page
tb,PDict3Parts-method Man page
TB_PDict-class Man page
tb,PreprocessedTB-method Man page
tb,TB_PDict-method Man page
tb.width Man page
tb.width,PDict3Parts-method Man page
tb.width,PreprocessedTB-method Man page
tb.width,TB_PDict-method Man page
threebands,character-method Man page
toComplex Man page
toComplex,DNAString-method Man page
toString,AlignedXStringSet0-method Man page
toString,MaskedXString-method Man page
toString,PairwiseAlignmentsSingleSubject-method Man page
toString,XString-method Man page
toString,XStringSet-method Man page
toString,XStringViews-method Man page
translate Man page
translate,DNAString-method Man page
translate,DNAStringSet-method Man page
translate,MaskedDNAString-method Man page
translate,MaskedRNAString-method Man page
translate,RNAString-method Man page
translate,RNAStringSet-method Man page
trimLRPatterns Man page
trimLRPatterns,character-method Man page
trimLRPatterns,XString-method Man page
trimLRPatterns,XStringSet-method Man page
trinucleotideFrequency Man page
Twobit Man page
Twobit-class Man page
type Man page
type,PairwiseAlignments-method Man page
type,PairwiseAlignmentsSingleSubjectSummary-method Man page
unaligned Man page
unaligned,AlignedXStringSet0-method Man page
uniqueLetters Man page
uniqueLetters,MaskedXString-method Man page
uniqueLetters,XString-method Man page
uniqueLetters,XStringSet-method Man page
uniqueLetters,XStringViews-method Man page
unitScale Man page
unlist,MIndex-method Man page
unlist,XStringSet-method Man page
unmasked Man page
unmasked,MaskedXString-method Man page
unmasked,MultipleAlignment-method Man page
unmasked,XString-method Man page
updateObject,XString-method Man page
updateObject,XStringSet-method Man page
vcountPattern Man page
vcountPattern,character-method Man page
vcountPattern,MaskedXString-method Man page
vcountPattern,XString-method Man page
vcountPattern,XStringSet-method Man page
vcountPattern,XStringViews-method Man page
vcountPDict Man page
vcountPDict,MaskedXString-method Man page
vcountPDict,XString-method Man page
vcountPDict,XStringSet-method Man page
vcountPDict,XStringViews-method Man page
Views,character-method Man page
Views,MaskedXString-method Man page
Views,PairwiseAlignmentsSingleSubject-method Man page
Views,XString-method Man page
vmatchPattern Man page
vmatchPattern,character-method Man page
vmatchPattern,MaskedXString-method Man page
vmatchPattern,XString-method Man page
vmatchPattern,XStringSet-method Man page
vmatchPattern,XStringViews-method Man page
vmatchPDict Man page
vmatchPDict,ANY-method Man page
vmatchPDict,MaskedXString-method Man page
vmatchPDict,XString-method Man page
vwhichPDict Man page
vwhichPDict,MaskedXString-method Man page
vwhichPDict,XString-method Man page
vwhichPDict,XStringSet-method Man page
vwhichPDict,XStringViews-method Man page
which.isMatchingAt Man page
which.isMatchingEndingAt Man page
which.isMatchingEndingAt,character-method Man page
which.isMatchingEndingAt,XString-method Man page
which.isMatchingEndingAt,XStringSet-method Man page
which.isMatchingStartingAt Man page
which.isMatchingStartingAt,character-method Man page
which.isMatchingStartingAt,XString-method Man page
which.isMatchingStartingAt,XStringSet-method Man page
whichPDict Man page
whichPDict,MaskedXString-method Man page
whichPDict,XString-method Man page
whichPDict,XStringSet-method Man page
whichPDict,XStringViews-method Man page
width0 Man page
width0,MIndex-method Man page
width,AlignedXStringSet0-method Man page
width,character-method Man page
width,PDict3Parts-method Man page
width,PDict-method Man page
width,PreprocessedTB-method Man page
writePairwiseAlignments Man page
write.phylip Man page
writeXStringSet Man page
wtPhiX174 Man page
xscat Man page
XString Man page
XString-class Man page
XStringCodec Man page
XStringCodec-class Man page
XStringPartialMatches-class Man page
[,XStringPartialMatches-method Man page
XStringQuality Man page
XStringQuality-class Man page
XStringSet Man page
XStringSet-class Man page
XStringSet-comparison Man page
XStringSet-io Man page
XStringSetList Man page
XStringSetList-class Man page
XStringViews Man page
==,XStringViews,character-method Man page
!=,XStringViews,character-method Man page
XStringViews-class Man page
==,XStringViews,XString-method Man page
!=,XStringViews,XString-method Man page
==,XStringViews,XStringViews-method Man page
!=,XStringViews,XStringViews-method Man page
==,XString,XString-method Man page
!=,XString,XString-method Man page
==,XString,XStringViews-method Man page
!=,XString,XStringViews-method Man page
yeastSEQCHR1 Man page

Files

Biostrings/.BBSoptions
Biostrings/CHANGES
Biostrings/DESCRIPTION
Biostrings/NAMESPACE
Biostrings/NEWS
Biostrings/R
Biostrings/R/00datacache.R Biostrings/R/AMINO_ACID_CODE.R Biostrings/R/AlignedXStringSet-class.R Biostrings/R/GENETIC_CODE.R Biostrings/R/IUPAC_CODE_MAP.R Biostrings/R/InDel-class.R Biostrings/R/MIndex-class.R Biostrings/R/MaskedXString-class.R Biostrings/R/MultipleAlignment.R Biostrings/R/PDict-class.R Biostrings/R/PairwiseAlignments-class.R Biostrings/R/PairwiseAlignments-io.R Biostrings/R/PairwiseAlignmentsSingleSubject-class.R Biostrings/R/QualityScaledXStringSet.R Biostrings/R/SparseList-class.R Biostrings/R/XString-class.R Biostrings/R/XStringCodec-class.R Biostrings/R/XStringPartialMatches-class.R Biostrings/R/XStringQuality-class.R Biostrings/R/XStringSet-class.R Biostrings/R/XStringSet-comparison.R Biostrings/R/XStringSet-io.R Biostrings/R/XStringSetList-class.R Biostrings/R/XStringViews-class.R Biostrings/R/align-utils.R Biostrings/R/chartr.R Biostrings/R/dinucleotideFrequencyTest.R Biostrings/R/findPalindromes.R Biostrings/R/getSeq.R Biostrings/R/injectHardMask.R Biostrings/R/letter.R Biostrings/R/letterFrequency.R Biostrings/R/lowlevel-matching.R Biostrings/R/maskMotif.R Biostrings/R/match-utils.R Biostrings/R/matchLRPatterns.R Biostrings/R/matchPDict.R Biostrings/R/matchPWM.R Biostrings/R/matchPattern.BOC.R Biostrings/R/matchPattern.BOC2.R Biostrings/R/matchPattern.R Biostrings/R/matchProbePair.R Biostrings/R/matchprobes.R Biostrings/R/misc.R Biostrings/R/needwunsQS.R Biostrings/R/padAndClip.R Biostrings/R/pairwiseAlignment.R Biostrings/R/pmatchPattern.R Biostrings/R/replaceAt.R Biostrings/R/replaceLetterAt.R Biostrings/R/reverseComplement.R Biostrings/R/seqtype.R Biostrings/R/stringDist.R Biostrings/R/toComplex.R Biostrings/R/translate.R Biostrings/R/trimLRPatterns.R Biostrings/R/unstrsplit-methods.R Biostrings/R/utils.R Biostrings/R/xscat.R Biostrings/R/zzz.R
Biostrings/TODO
Biostrings/build
Biostrings/build/vignette.rds
Biostrings/data
Biostrings/data/BLOSUM100.rda
Biostrings/data/BLOSUM45.rda
Biostrings/data/BLOSUM50.rda
Biostrings/data/BLOSUM62.rda
Biostrings/data/BLOSUM80.rda
Biostrings/data/HNF4alpha.rda
Biostrings/data/PAM120.rda
Biostrings/data/PAM250.rda
Biostrings/data/PAM30.rda
Biostrings/data/PAM40.rda
Biostrings/data/PAM70.rda
Biostrings/data/phiX174Phage.rda
Biostrings/data/srPhiX174.rda
Biostrings/data/yeastSEQCHR1.rda
Biostrings/devtools
Biostrings/devtools/rgrep-tip.txt
Biostrings/inst
Biostrings/inst/doc
Biostrings/inst/doc/Biostrings2Classes.R
Biostrings/inst/doc/Biostrings2Classes.Rnw
Biostrings/inst/doc/Biostrings2Classes.pdf
Biostrings/inst/doc/BiostringsQuickOverview.Rnw
Biostrings/inst/doc/BiostringsQuickOverview.pdf
Biostrings/inst/doc/MultipleAlignments.R
Biostrings/inst/doc/MultipleAlignments.Rnw
Biostrings/inst/doc/MultipleAlignments.pdf
Biostrings/inst/doc/PairwiseAlignments.R
Biostrings/inst/doc/PairwiseAlignments.Rnw
Biostrings/inst/doc/PairwiseAlignments.pdf
Biostrings/inst/doc/matchprobes.R
Biostrings/inst/doc/matchprobes.Rnw
Biostrings/inst/doc/matchprobes.pdf
Biostrings/inst/extdata
Biostrings/inst/extdata/Phylip.txt
Biostrings/inst/extdata/README
Biostrings/inst/extdata/Sc.fa
Biostrings/inst/extdata/Sp.fa
Biostrings/inst/extdata/dm3_upstream2000.fa.gz
Biostrings/inst/extdata/fastaEx.fa
Biostrings/inst/extdata/hg18chr8_gap.txt
Biostrings/inst/extdata/hg18chrY_gap.txt
Biostrings/inst/extdata/msx2_mRNA.aln
Biostrings/inst/extdata/s_1_sequence.txt
Biostrings/inst/extdata/someORF.fa
Biostrings/inst/extdata/someORF.fa.gz
Biostrings/inst/include
Biostrings/inst/include/Biostrings_defines.h
Biostrings/inst/include/Biostrings_interface.h
Biostrings/inst/include/_Biostrings_stubs.c
Biostrings/inst/unitTests
Biostrings/inst/unitTests/test_MultipleAlignment.R
Biostrings/inst/unitTests/test_XString.R
Biostrings/inst/unitTests/test_XStringSet.R
Biostrings/inst/unitTests/test_XStringSetList.R
Biostrings/inst/unitTests/test_findPalindromes.R
Biostrings/inst/unitTests/test_matchDNAPattern.R.FIXME
Biostrings/inst/unitTests/test_matchPDict.R
Biostrings/inst/unitTests/test_pairwiseAlignment.R
Biostrings/inst/unitTests/test_twoWayAlphabetFrequency.R
Biostrings/man
Biostrings/man/AAString-class.Rd Biostrings/man/AMINO_ACID_CODE.Rd Biostrings/man/AlignedXStringSet-class.Rd Biostrings/man/BOC_SubjectString-class.Rd Biostrings/man/Biostrings-internals.Rd Biostrings/man/DNAString-class.Rd Biostrings/man/GENETIC_CODE.Rd Biostrings/man/HNF4alpha.Rd Biostrings/man/IUPAC_CODE_MAP.Rd Biostrings/man/InDel-class.Rd Biostrings/man/MIndex-class.Rd Biostrings/man/MaskedXString-class.Rd Biostrings/man/MultipleAlignment-class.Rd Biostrings/man/PDict-class.Rd Biostrings/man/PairwiseAlignments-class.Rd Biostrings/man/PairwiseAlignments-io.Rd Biostrings/man/QualityScaledXStringSet-class.Rd Biostrings/man/RNAString-class.Rd Biostrings/man/XString-class.Rd Biostrings/man/XStringPartialMatches-class.Rd Biostrings/man/XStringQuality-class.Rd Biostrings/man/XStringSet-class.Rd Biostrings/man/XStringSet-comparison.Rd Biostrings/man/XStringSet-io.Rd Biostrings/man/XStringSetList-class.Rd Biostrings/man/XStringViews-class.Rd Biostrings/man/align-utils.Rd Biostrings/man/chartr.Rd Biostrings/man/detail.Rd Biostrings/man/dinucleotideFrequencyTest.Rd Biostrings/man/findPalindromes.Rd Biostrings/man/getSeq.Rd Biostrings/man/gregexpr2.Rd Biostrings/man/injectHardMask.Rd Biostrings/man/letter.Rd Biostrings/man/letterFrequency.Rd Biostrings/man/longestConsecutive.Rd Biostrings/man/lowlevel-matching.Rd Biostrings/man/maskMotif.Rd Biostrings/man/match-utils.Rd Biostrings/man/matchLRPatterns.Rd Biostrings/man/matchPDict-exact.Rd Biostrings/man/matchPDict-inexact.Rd Biostrings/man/matchPWM.Rd Biostrings/man/matchPattern.Rd Biostrings/man/matchProbePair.Rd Biostrings/man/matchprobes.Rd Biostrings/man/misc.Rd Biostrings/man/needwunsQS.Rd Biostrings/man/nucleotideFrequency.Rd Biostrings/man/padAndClip.Rd Biostrings/man/pairwiseAlignment.Rd Biostrings/man/phiX174Phage.Rd Biostrings/man/pid.Rd Biostrings/man/pmatchPattern.Rd Biostrings/man/replaceAt.Rd Biostrings/man/replaceLetterAt.Rd Biostrings/man/reverseComplement.Rd Biostrings/man/stringDist.Rd Biostrings/man/substitution_matrices.Rd Biostrings/man/toComplex.Rd Biostrings/man/translate.Rd Biostrings/man/trimLRPatterns.Rd Biostrings/man/xscat.Rd Biostrings/man/yeastSEQCHR1.Rd
Biostrings/src
Biostrings/src/BAB_class.c
Biostrings/src/Biostrings.h
Biostrings/src/BitMatrix.c
Biostrings/src/IRanges_stubs.c
Biostrings/src/MIndex_class.c
Biostrings/src/PreprocessedTB_class.c
Biostrings/src/R_init_Biostrings.c
Biostrings/src/RoSeqs_utils.c
Biostrings/src/S4Vectors_stubs.c
Biostrings/src/SparseList_utils.c
Biostrings/src/XStringSetList_class.c
Biostrings/src/XStringSet_class.c
Biostrings/src/XStringSet_io.c
Biostrings/src/XString_class.c
Biostrings/src/XVector_stubs.c
Biostrings/src/align_needwunsQS.c
Biostrings/src/align_pairwiseAlignment.c
Biostrings/src/align_utils.c
Biostrings/src/find_palindromes.c
Biostrings/src/gtestsim.c
Biostrings/src/inject_code.c
Biostrings/src/letter_frequency.c
Biostrings/src/lowlevel_matching.c
Biostrings/src/match_PWM.c
Biostrings/src/match_pattern.c
Biostrings/src/match_pattern_boyermoore.c
Biostrings/src/match_pattern_indels.c
Biostrings/src/match_pattern_shiftor.c
Biostrings/src/match_pdict.c
Biostrings/src/match_pdict_ACtree2.c
Biostrings/src/match_pdict_Twobit.c
Biostrings/src/match_pdict_utils.c
Biostrings/src/match_reporting.c
Biostrings/src/matchprobes.c
Biostrings/src/pmatchPattern.c
Biostrings/src/replaceAt.c
Biostrings/src/replace_letter_at.c
Biostrings/src/strutils.c
Biostrings/src/translate.c
Biostrings/src/unstrsplit_methods.c
Biostrings/src/utils.c
Biostrings/src/xscat.c
Biostrings/tests
Biostrings/tests/run_unitTests.R
Biostrings/vignettes
Biostrings/vignettes/Biostrings2Classes.Rnw
Biostrings/vignettes/BiostringsQuickOverview.Rnw
Biostrings/vignettes/MultipleAlignments.Rnw
Biostrings/vignettes/PairwiseAlignments.Rnw
Biostrings/vignettes/SolexaYi2-benchmark.txt
Biostrings/vignettes/matchprobes.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.