# Efficient manipulation of biological strings

## Documentation for package ‘Biostrings’ version 2.60.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P Q R S T U V W X Y misc

## -- A --

AAMultipleAlignment | MultipleAlignment objects
AAMultipleAlignment-class | MultipleAlignment objects
AAString | AAString objects
AAString-class | AAString objects
AAStringSet | XStringSet objects
AAStringSet-class | XStringSet objects
AAStringSetList | XStringSetList objects
AAStringSetList-class | XStringSetList objects
AA_ALPHABET | AAString objects
AA_PROTEINOGENIC | AAString objects
AA_STANDARD | AAString objects
ACtree2 | PDict objects
ACtree2-class | PDict objects
align-utils | Utility functions related to sequence alignment
aligned | AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method | AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0-class | AlignedXStringSet and QualityAlignedXStringSet objects
alphabet | BString objects
alphabet-method | BString objects
alphabet-method | PhredQuality, SolexaQuality and IlluminaQuality objects
alphabetFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
alphabetFrequency-method | MultipleAlignment objects
alphabetFrequency-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
AMINO_ACID_CODE | The Single-Letter Amino Acid Code
anyNA-method | Comparing and ordering the elements in one or more XStringSet objects
as.character-method | AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method | MaskedXString objects
as.character-method | MultipleAlignment objects
as.character-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
as.character-method | BString objects
as.character-method | XStringSet objects
as.character-method | The XStringViews class
as.data.frame-method | XStringSet objects
as.data.frame-method | The XStringViews class
as.factor-method | XStringSet objects
as.list-method | PDict objects
as.matrix-method | MultipleAlignment objects
as.matrix-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
as.matrix-method | PhredQuality, SolexaQuality and IlluminaQuality objects
as.matrix-method | XStringSet objects
as.matrix-method | The XStringViews class
as.vector-method | BString objects
as.vector-method | PhredQuality, SolexaQuality and IlluminaQuality objects
as.vector-method | XStringSet objects

## -- B --

BLOSUM100 | Scoring matrices
BLOSUM45 | Scoring matrices
BLOSUM50 | Scoring matrices
BLOSUM62 | Scoring matrices
BLOSUM80 | Scoring matrices
BString | BString objects
BString-class | BString objects
BStringSet | XStringSet objects
BStringSet-class | XStringSet objects
BStringSetList | XStringSetList objects
BStringSetList-class | XStringSetList objects
ByPos_MIndex-class | MIndex objects

## -- C --

chartr | Replace letters in a sequence or set of sequences
chartr-method | Replace letters in a sequence or set of sequences
class:AAMultipleAlignment | MultipleAlignment objects
class:AAString | AAString objects
class:AAStringSet | XStringSet objects
class:AAStringSetList | XStringSetList objects
class:ACtree2 | PDict objects
class:AlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
class:AlignedXStringSet0 | AlignedXStringSet and QualityAlignedXStringSet objects
class:BString | BString objects
class:BStringSet | XStringSet objects
class:BStringSetList | XStringSetList objects
class:ByPos_MIndex | MIndex objects
class:DNAMultipleAlignment | MultipleAlignment objects
class:DNAString | DNAString objects
class:DNAStringSet | XStringSet objects
class:DNAStringSetList | XStringSetList objects
class:Expanded_TB_PDict | PDict objects
class:IlluminaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
class:InDel | InDel objects
class:MaskedAAString | MaskedXString objects
class:MaskedBString | MaskedXString objects
class:MaskedDNAString | MaskedXString objects
class:MaskedRNAString | MaskedXString objects
class:MaskedXString | MaskedXString objects
class:MIndex | MIndex objects
class:MTB_PDict | PDict objects
class:MultipleAlignment | MultipleAlignment objects
class:PairwiseAlignments | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubjectSummary | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PDict | PDict objects
class:PDict3Parts | PDict objects
class:PhredQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
class:PreprocessedTB | PDict objects
class:QualityAlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
class:QualityScaledAAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledBStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledRNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:QualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
class:RNAMultipleAlignment | MultipleAlignment objects
class:RNAString | RNAString objects
class:RNAStringSet | XStringSet objects
class:RNAStringSetList | XStringSetList objects
class:SolexaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
class:TB_PDict | PDict objects
class:Twobit | PDict objects
class:XString | BString objects
class:XStringPartialMatches | XStringPartialMatches objects
class:XStringQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
class:XStringSet | XStringSet objects
class:XStringSetList | XStringSetList objects
class:XStringViews | The XStringViews class
codons | Translating DNA/RNA sequences
codons-method | Translating DNA/RNA sequences
coerce-method | MIndex objects
coerce-method | MaskedXString objects
coerce-method | MultipleAlignment objects
coerce-method | BString objects
coerce-method | PhredQuality, SolexaQuality and IlluminaQuality objects
coerce-method | XStringSet objects
coerce-method | The XStringViews class
collapse-method | MaskedXString objects
colmask | MultipleAlignment objects
colmask-method | MultipleAlignment objects
colmask<- | MultipleAlignment objects
colmask<--method | MultipleAlignment objects
compareStrings | Utility functions related to sequence alignment
compareStrings-method | Utility functions related to sequence alignment
complement | Sequence reversing and complementing
complement-method | Sequence reversing and complementing
computeAllFlinks | PDict objects
computeAllFlinks-method | PDict objects
consensusMatrix | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusMatrix-method | MultipleAlignment objects
consensusMatrix-method | Utility functions related to sequence alignment
consensusMatrix-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusString-method | MultipleAlignment objects
consensusString-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
consensusViews | MultipleAlignment objects
consensusViews-method | MultipleAlignment objects
countPattern | String searching functions
countPattern-method | String searching functions
countPDict | Matching a dictionary of patterns against a reference
countPDict-method | Matching a dictionary of patterns against a reference
countPWM | PWM creating, matching, and related utilities
countPWM-method | PWM creating, matching, and related utilities
coverage-method | Utility functions related to sequence alignment
coverage-method | Utility functions operating on the matches returned by a high-level matching function

## -- D --

deletion | InDel objects
deletion-method | InDel objects
deletion-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
detail | Show (display) detailed object content
detail-method | MultipleAlignment objects
dim-method | MultipleAlignment objects
dinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
dinucleotideFrequencyTest | Pearson's chi-squared Test and G-tests for String Position Dependence
dinucleotideFrequencyTest-method | Pearson's chi-squared Test and G-tests for String Position Dependence
DNAMultipleAlignment | MultipleAlignment objects
DNAMultipleAlignment-class | MultipleAlignment objects
DNAString | DNAString objects
DNAString-class | DNAString objects
DNAStringSet | XStringSet objects
DNAStringSet-class | XStringSet objects
DNAStringSetList | XStringSetList objects
DNAStringSetList-class | XStringSetList objects
DNA_ALPHABET | DNAString objects
DNA_BASES | DNAString objects
duplicated-method | PDict objects

## -- E --

elementNROWS-method | MIndex objects
encoding | PhredQuality, SolexaQuality and IlluminaQuality objects
encoding-method | PhredQuality, SolexaQuality and IlluminaQuality objects
end-method | AlignedXStringSet and QualityAlignedXStringSet objects
endIndex | MIndex objects
endIndex-method | MIndex objects
errorSubstitutionMatrices | Scoring matrices
Expanded_TB_PDict | PDict objects
Expanded_TB_PDict-class | PDict objects
extractAllMatches | Matching a dictionary of patterns against a reference
extractAt | Extract/replace arbitrary substrings from/in a string or set of strings.
extractAt-method | Extract/replace arbitrary substrings from/in a string or set of strings.

## -- F --

fasta.index | Read/write an XStringSet object from/to a file
fasta.seqlengths | Read/write an XStringSet object from/to a file
fastq.geometry | Read/write an XStringSet object from/to a file
fastq.seqlengths | Read/write an XStringSet object from/to a file
findPalindromes | Searching a sequence for palindromes
findPalindromes-method | Searching a sequence for palindromes

## -- G --

gaps-method | MaskedXString objects
GENETIC_CODE | The Standard Genetic Code and its known variants
GENETIC_CODE_TABLE | The Standard Genetic Code and its known variants
getGeneticCode | The Standard Genetic Code and its known variants
getSeq | getSeq
gregexpr2 | A replacement for R standard gregexpr function

## -- H --

hasAllFlinks | PDict objects
hasAllFlinks-method | PDict objects
hasLetterAt | Low-level matching functions
hasOnlyBaseLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
hasOnlyBaseLetters-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
head-method | PDict objects
HNF4alpha | Known HNF4alpha binding sequences

## -- I --

IlluminaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
IlluminaQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects
InDel | InDel objects
indel | AlignedXStringSet and QualityAlignedXStringSet objects
InDel-class | InDel objects
indel-method | AlignedXStringSet and QualityAlignedXStringSet objects
indel-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
initialize-method | PDict objects
injectHardMask | Injecting a hard mask in a sequence
injectHardMask-method | Injecting a hard mask in a sequence
insertion | InDel objects
insertion-method | InDel objects
insertion-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
is.na-method | Comparing and ordering the elements in one or more XStringSet objects
isMatchingAt | Low-level matching functions
isMatchingEndingAt | Low-level matching functions
isMatchingEndingAt-method | Low-level matching functions
isMatchingStartingAt | Low-level matching functions
isMatchingStartingAt-method | Low-level matching functions
IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet

## -- L --

lcprefix | Longest Common Prefix/Suffix/Substring searching functions
lcprefix-method | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr | Longest Common Prefix/Suffix/Substring searching functions
lcsubstr-method | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix | Longest Common Prefix/Suffix/Substring searching functions
lcsuffix-method | Longest Common Prefix/Suffix/Substring searching functions
length-method | MIndex objects
length-method | MaskedXString objects
length-method | PDict objects
length-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
letter | Subsetting a string
letter-method | Subsetting a string
letterFrequency | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
letterFrequency-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
letterFrequencyInSlidingView | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
letterFrequencyInSlidingView-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
longestConsecutive | Obtain the length of the longest substring containing only 'letter'
lowlevel-matching | Low-level matching functions

## -- M --

mask | Masking by content (or by position)
MaskedAAString | MaskedXString objects
MaskedAAString-class | MaskedXString objects
MaskedBString | MaskedXString objects
MaskedBString-class | MaskedXString objects
maskeddim | MultipleAlignment objects
maskeddim-method | MultipleAlignment objects
MaskedDNAString | MaskedXString objects
MaskedDNAString-class | MaskedXString objects
maskedncol | MultipleAlignment objects
maskedncol-method | MultipleAlignment objects
maskednrow | MultipleAlignment objects
maskednrow-method | MultipleAlignment objects
maskedratio-method | MaskedXString objects
maskedratio-method | MultipleAlignment objects
MaskedRNAString | MaskedXString objects
MaskedRNAString-class | MaskedXString objects
maskedwidth-method | MaskedXString objects
MaskedXString | MaskedXString objects
MaskedXString-class | MaskedXString objects
maskGaps | MultipleAlignment objects
maskGaps-method | MultipleAlignment objects
maskMotif | Masking by content (or by position)
maskMotif-method | MultipleAlignment objects
maskMotif-method | Masking by content (or by position)
masks | MaskedXString objects
masks-method | MaskedXString objects
masks<- | MaskedXString objects
masks<--method | MaskedXString objects
match-method | Comparing and ordering the elements in one or more XStringSet objects
match-utils | Utility functions operating on the matches returned by a high-level matching function
matchLRPatterns | Find paired matches in a sequence
matchLRPatterns-method | Find paired matches in a sequence
matchPattern | String searching functions
matchPattern-method | String searching functions
matchPDict | Matching a dictionary of patterns against a reference
matchPDict-exact | Matching a dictionary of patterns against a reference
matchPDict-inexact | Inexact matching with matchPDict()/countPDict()/whichPDict()
matchPDict-method | Matching a dictionary of patterns against a reference
matchProbePair | Find "theoretical amplicons" mapped to a probe pair
matchProbePair-method | Find "theoretical amplicons" mapped to a probe pair
matchprobes | A function to match a query sequence to the sequences of a set of probes.
matchPWM | PWM creating, matching, and related utilities
matchPWM-method | PWM creating, matching, and related utilities
maxScore | PWM creating, matching, and related utilities
maxScore-method | PWM creating, matching, and related utilities
maxWeights | PWM creating, matching, and related utilities
maxWeights-method | PWM creating, matching, and related utilities
mergeIUPACLetters | The IUPAC Extended Genetic Alphabet
MIndex | MIndex objects
MIndex-class | MIndex objects
minScore | PWM creating, matching, and related utilities
minScore-method | PWM creating, matching, and related utilities
minWeights | PWM creating, matching, and related utilities
minWeights-method | PWM creating, matching, and related utilities
misc | Some miscellaneous stuff
mismatch | Utility functions operating on the matches returned by a high-level matching function
mismatch-method | Utility functions related to sequence alignment
mismatch-method | Utility functions operating on the matches returned by a high-level matching function
mismatchSummary | Utility functions related to sequence alignment
mismatchSummary-method | Utility functions related to sequence alignment
mismatchTable | Utility functions related to sequence alignment
mismatchTable-method | Utility functions related to sequence alignment
mkAllStrings | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
MTB_PDict | PDict objects
MTB_PDict-class | PDict objects
MultipleAlignment | MultipleAlignment objects
MultipleAlignment-class | MultipleAlignment objects

## -- N --

N50 | Some miscellaneous stuff
names-method | MIndex objects
names-method | PDict objects
names<--method | MIndex objects
names<--method | PDict objects
narrow-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
narrow-method | XStringSet objects
nchar-method | AlignedXStringSet and QualityAlignedXStringSet objects
nchar-method | MaskedXString objects
nchar-method | MultipleAlignment objects
nchar-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nchar-method | BString objects
nchar-method | XStringSet objects
nchar-method | XStringSetList objects
nchar-method | The XStringViews class
ncol-method | MultipleAlignment objects
nedit | Utility functions related to sequence alignment
nedit-method | Utility functions related to sequence alignment
neditAt | Low-level matching functions
neditEndingAt | Low-level matching functions
neditEndingAt-method | Low-level matching functions
neditStartingAt | Low-level matching functions
neditStartingAt-method | Low-level matching functions
needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment
needwunsQS-method | (Deprecated) Needleman-Wunsch Global Alignment
nindel | AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method | AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nmatch | Utility functions operating on the matches returned by a high-level matching function
nmatch-method | Utility functions related to sequence alignment
nmatch-method | Utility functions operating on the matches returned by a high-level matching function
nmismatch | Utility functions operating on the matches returned by a high-level matching function
nmismatch-method | Utility functions related to sequence alignment
nmismatch-method | Utility functions operating on the matches returned by a high-level matching function
nnodes | PDict objects
nnodes-method | PDict objects
nrow-method | MultipleAlignment objects
nucleotideFrequencyAt | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
nucleotideFrequencyAt-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
nucleotideSubstitutionMatrix | Scoring matrices

## -- O --

oligonucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideFrequency-method | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
oligonucleotideTransitions | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)

## -- P --

padAndClip | Pad and clip strings
pairwiseAlignment | Optimal Pairwise Alignment
pairwiseAlignment-method | Optimal Pairwise Alignment
PairwiseAlignments | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io | Write a PairwiseAlignments object to a file
PairwiseAlignments-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
palindromeArmLength | Searching a sequence for palindromes
palindromeArmLength-method | Searching a sequence for palindromes
palindromeLeftArm | Searching a sequence for palindromes
palindromeLeftArm-method | Searching a sequence for palindromes
palindromeRightArm | Searching a sequence for palindromes
palindromeRightArm-method | Searching a sequence for palindromes
PAM120 | Scoring matrices
PAM250 | Scoring matrices
PAM30 | Scoring matrices
PAM40 | Scoring matrices
PAM70 | Scoring matrices
parallelVectorNames-method | AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method | AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
parallel_slot_names-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
pattern | XStringPartialMatches objects
pattern-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
pattern-method | XStringPartialMatches objects
patternFrequency | PDict objects
patternFrequency-method | PDict objects
pcompare-method | Comparing and ordering the elements in one or more XStringSet objects
PDict | PDict objects
PDict-class | PDict objects
PDict-method | PDict objects
PDict3Parts | PDict objects
PDict3Parts-class | PDict objects
phiX174Phage | Versions of bacteriophage phiX174 complete genome and sample short reads
PhredQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
PhredQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects
pid | Percent Sequence Identity
pid-method | Percent Sequence Identity
pmatchPattern | Longest Common Prefix/Suffix/Substring searching functions
pmatchPattern-method | Longest Common Prefix/Suffix/Substring searching functions
PreprocessedTB | PDict objects
PreprocessedTB-class | PDict objects
print.needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment
PWM | PWM creating, matching, and related utilities
PWM-method | PWM creating, matching, and related utilities
PWMscoreStartingAt | PWM creating, matching, and related utilities

## -- Q --

quality | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
quality-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityAlignedXStringSet | AlignedXStringSet and QualityAlignedXStringSet objects
QualityAlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects
QualityScaledAAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledAAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledBStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledBStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledDNAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledRNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledRNAStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
QualityScaledXStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
qualitySubstitutionMatrices | Scoring matrices
quPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads

## -- R --

ranges-method | AlignedXStringSet and QualityAlignedXStringSet objects
readAAMultipleAlignment | MultipleAlignment objects
readAAStringSet | Read/write an XStringSet object from/to a file
readBStringSet | Read/write an XStringSet object from/to a file
readDNAMultipleAlignment | MultipleAlignment objects
readDNAStringSet | Read/write an XStringSet object from/to a file
readQualityScaledDNAStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
readRNAMultipleAlignment | MultipleAlignment objects
readRNAStringSet | Read/write an XStringSet object from/to a file
replaceAmbiguities | Replace letters in a sequence or set of sequences
replaceAt | Extract/replace arbitrary substrings from/in a string or set of strings.
replaceAt-method | Extract/replace arbitrary substrings from/in a string or set of strings.
replaceLetterAt | Replacing letters in a sequence (or set of sequences) at some specified locations
replaceLetterAt-method | Replacing letters in a sequence (or set of sequences) at some specified locations
reverse-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
reverse-method | Sequence reversing and complementing
reverseComplement | Sequence reversing and complementing
reverseComplement-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
reverseComplement-method | PWM creating, matching, and related utilities
reverseComplement-method | Sequence reversing and complementing
RNAMultipleAlignment | MultipleAlignment objects
RNAMultipleAlignment-class | MultipleAlignment objects
RNAString | RNAString objects
RNAString-class | RNAString objects
RNAStringSet | XStringSet objects
RNAStringSet-class | XStringSet objects
RNAStringSetList | XStringSetList objects
RNAStringSetList-class | XStringSetList objects
RNA_ALPHABET | RNAString objects
RNA_BASES | RNAString objects
RNA_GENETIC_CODE | The Standard Genetic Code and its known variants
rowmask | MultipleAlignment objects
rowmask-method | MultipleAlignment objects
rowmask<- | MultipleAlignment objects
rowmask<--method | MultipleAlignment objects
rownames-method | MultipleAlignment objects
rownames<--method | MultipleAlignment objects

## -- S --

saveXStringSet | Read/write an XStringSet object from/to a file
score-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
seqinfo | seqinfo method for DNAStringSet objects
seqinfo-method | seqinfo method for DNAStringSet objects
seqinfo<--method | seqinfo method for DNAStringSet objects
seqtype-method | AlignedXStringSet and QualityAlignedXStringSet objects
seqtype-method | MaskedXString objects
seqtype-method | MultipleAlignment objects
seqtype-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
seqtype-method | BString objects
seqtype-method | XStringSet objects
seqtype-method | XStringSetList objects
seqtype-method | The XStringViews class
seqtype<--method | MaskedXString objects
seqtype<--method | BString objects
seqtype<--method | XStringSet objects
seqtype<--method | XStringSetList objects
seqtype<--method | The XStringViews class
show-method | AlignedXStringSet and QualityAlignedXStringSet objects
show-method | MIndex objects
show-method | MaskedXString objects
show-method | MultipleAlignment objects
show-method | PDict objects
show-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
show-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
show-method | BString objects
show-method | XStringPartialMatches objects
show-method | XStringSet objects
show-method | XStringSetList objects
show-method | The XStringViews class
showAsCell-method | BString objects
showAsCell-method | XStringSet objects
SolexaQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
SolexaQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects
srPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads
stackStrings | Pad and clip strings
start-method | AlignedXStringSet and QualityAlignedXStringSet objects
startIndex | MIndex objects
startIndex-method | MIndex objects
stringDist | String Distance/Alignment Score Matrix
stringDist-method | String Distance/Alignment Score Matrix
subject-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
subpatterns | XStringPartialMatches objects
subpatterns-method | XStringPartialMatches objects
subseq-method | MaskedXString objects
subseq-method | XStringSet objects
subseq<--method | XStringSet objects
substitution.matrices | Scoring matrices
substr-method | BString objects
substring-method | BString objects
summary-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- T --

tail-method | PDict objects
tb | PDict objects
tb-method | PDict objects
tb.width | PDict objects
tb.width-method | PDict objects
TB_PDict | PDict objects
TB_PDict-class | PDict objects
threebands-method | XStringSet objects
toComplex | Turning a DNA sequence into a vector of complex numbers
toComplex-method | Turning a DNA sequence into a vector of complex numbers
toString-method | AlignedXStringSet and QualityAlignedXStringSet objects
toString-method | MaskedXString objects
toString-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
toString-method | BString objects
toString-method | XStringSet objects
toString-method | The XStringViews class
translate | Translating DNA/RNA sequences
translate-method | Translating DNA/RNA sequences
trimLRPatterns | Trim Flanking Patterns from Sequences
trimLRPatterns-method | Trim Flanking Patterns from Sequences
trinucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions)
Twobit | PDict objects
Twobit-class | PDict objects
type | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
type-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

## -- U --

unaligned | AlignedXStringSet and QualityAlignedXStringSet objects
unaligned-method | AlignedXStringSet and QualityAlignedXStringSet objects
uniqueLetters | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
uniqueLetters-method | Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences
unitScale | PWM creating, matching, and related utilities
unlist-method | MIndex objects
unlist-method | XStringSet objects
unmasked | MaskedXString objects
unmasked-method | MaskedXString objects
unmasked-method | MultipleAlignment objects
updateObject-method | BString objects
updateObject-method | XStringSet objects

## -- V --

vcountPattern | String searching functions
vcountPattern-method | String searching functions
vcountPDict | Matching a dictionary of patterns against a reference
vcountPDict-method | Matching a dictionary of patterns against a reference
Views-method | MaskedXString objects
Views-method | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
Views-method | The XStringViews class
vmatchPattern | String searching functions
vmatchPattern-method | String searching functions
vmatchPDict | Matching a dictionary of patterns against a reference
vmatchPDict-method | Matching a dictionary of patterns against a reference
vwhichPDict | Matching a dictionary of patterns against a reference
vwhichPDict-method | Matching a dictionary of patterns against a reference

## -- W --

which.isMatchingAt | Low-level matching functions
which.isMatchingEndingAt | Low-level matching functions
which.isMatchingEndingAt-method | Low-level matching functions
which.isMatchingStartingAt | Low-level matching functions
which.isMatchingStartingAt-method | Low-level matching functions
whichPDict | Matching a dictionary of patterns against a reference
whichPDict-method | Matching a dictionary of patterns against a reference
width-method | AlignedXStringSet and QualityAlignedXStringSet objects
width-method | PDict objects
width-method | XStringSet objects
width0 | MIndex objects
width0-method | MIndex objects
windows-method | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
windows-method | XStringSet objects
write.phylip | MultipleAlignment objects
writePairwiseAlignments | Write a PairwiseAlignments object to a file
writeQualityScaledXStringSet | QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
writeXStringSet | Read/write an XStringSet object from/to a file
wtPhiX174 | Versions of bacteriophage phiX174 complete genome and sample short reads

## -- X --

xscat | Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
XString | BString objects
XString-class | BString objects
XStringPartialMatches-class | XStringPartialMatches objects
XStringQuality | PhredQuality, SolexaQuality and IlluminaQuality objects
XStringQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects
XStringSet | XStringSet objects
XStringSet-class | XStringSet objects
XStringSet-comparison | Comparing and ordering the elements in one or more XStringSet objects
XStringSet-io | Read/write an XStringSet object from/to a file
XStringSetList | XStringSetList objects
XStringSetList-class | XStringSetList objects
XStringViews | The XStringViews class
XStringViews-class | The XStringViews class

## -- Y --

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

## -- misc --

!=-method | BString objects
!=-method | The XStringViews class
.inplaceReplaceLetterAt | Replacing letters in a sequence (or set of sequences) at some specified locations
==-method | BString objects
==-method | The XStringViews class
[-method | XStringPartialMatches objects
[[-method | MIndex objects
[[-method | PDict objects