Efficient manipulation of biological strings

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Documentation for package ‘Biostrings’ version 2.58.0

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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
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