String objects representing biological sequences, and matching algorithms


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Documentation for package ‘Biostrings’ version 2.20.1

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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 --

AAKeySortedData Data Dictionaries with XString-based Keys
AAKeySortedData-class Data Dictionaries with XString-based Keys
AAKeySortedDataList List of Data Dictionaries with XString-based Keys
AAKeySortedDataList-class List of Data Dictionaries with XString-based Keys
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_WCP Weighted Clustered Positions (WCP) objects
AA_WCP-class Weighted Clustered Positions (WCP) objects
ACtree2 PDict objects
ACtree2-class PDict objects
adjacentViews Basic functions for creating or modifying XStringViews objects
align-utils Utility functions related to sequence alignment
aligned AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary 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
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
append-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
as.character-method AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method MaskedXString objects
as.character-method MultipleAlignment objects
as.character-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
as.character-method BString objects
as.character-method XStringSet objects
as.character-method The XStringViews class
as.integer-method PhredQuality and SolexaQuality objects
as.list-method PDict objects
as.matrix-method MultipleAlignment objects
as.matrix-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
as.matrix-method PhredQuality and SolexaQuality objects
as.matrix-method XStringSet objects
as.matrix-method The XStringViews class
as.numeric-method PhredQuality and SolexaQuality objects

-- B --

basecontent Obtain the ATCG content of a gene
BKeySortedData Data Dictionaries with XString-based Keys
BKeySortedData-class Data Dictionaries with XString-based Keys
BKeySortedDataList List of Data Dictionaries with XString-based Keys
BKeySortedDataList-class List of Data Dictionaries with XString-based Keys
BLOSUM100 Scoring matrices
BLOSUM45 Scoring matrices
BLOSUM50 Scoring matrices
BLOSUM62 Scoring matrices
BLOSUM80 Scoring matrices
BOC2_SubjectString BOC\_SubjectString and BOC2\_SubjectString objects
BOC2_SubjectString-class BOC\_SubjectString and BOC2\_SubjectString objects
BOC_SubjectString BOC\_SubjectString and BOC2\_SubjectString objects
BOC_SubjectString-class BOC\_SubjectString and BOC2\_SubjectString objects
BString BString objects
BString-class BString objects
BStringSet XStringSet objects
BStringSet-class XStringSet objects
BStringSetList XStringSetList objects
BStringSetList-class XStringSetList objects
BStringViews Basic functions for creating or modifying XStringViews objects
BStringViews-method Basic functions for creating or modifying XStringViews objects
ByPos_MIndex-class MIndex objects
B_WCP Weighted Clustered Positions (WCP) objects
B_WCP-class Weighted Clustered Positions (WCP) objects

-- C --

cDNA DNA/RNA transcription and translation
CharacterToFASTArecords Read/write an XStringSet object from/to a file
chartr-method Translating letters of a sequence
class:AAKeySortedData Data Dictionaries with XString-based Keys
class:AAKeySortedDataList List of Data Dictionaries with XString-based Keys
class:AAMultipleAlignment MultipleAlignment objects
class:AAString AAString objects
class:AAStringSet XStringSet objects
class:AAStringSetList XStringSetList objects
class:AA_WCP Weighted Clustered Positions (WCP) objects
class:ACtree2 PDict objects
class:AlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
class:AlignedXStringSet0 AlignedXStringSet and QualityAlignedXStringSet objects
class:BKeySortedData Data Dictionaries with XString-based Keys
class:BKeySortedDataList List of Data Dictionaries with XString-based Keys
class:BOC2_SubjectString BOC\_SubjectString and BOC2\_SubjectString objects
class:BOC_SubjectString BOC\_SubjectString and BOC2\_SubjectString objects
class:BString BString objects
class:BStringSet XStringSet objects
class:BStringSetList XStringSetList objects
class:ByPos_MIndex MIndex objects
class:B_WCP Weighted Clustered Positions (WCP) objects
class:DNAKeySortedData Data Dictionaries with XString-based Keys
class:DNAKeySortedDataList List of Data Dictionaries with XString-based Keys
class:DNAMultipleAlignment MultipleAlignment objects
class:DNAString DNAString objects
class:DNAStringSet XStringSet objects
class:DNAStringSetList XStringSetList objects
class:DNA_WCP Weighted Clustered Positions (WCP) objects
class:Expanded_TB_PDict PDict 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:PairwiseAlignedFixedSubject PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PairwiseAlignedFixedSubjectSummary PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PairwiseAlignedXStringSet PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
class:PDict PDict objects
class:PDict3Parts PDict objects
class:PhredQuality PhredQuality and SolexaQuality 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:RNAKeySortedData Data Dictionaries with XString-based Keys
class:RNAKeySortedDataList List of Data Dictionaries with XString-based Keys
class:RNAMultipleAlignment MultipleAlignment objects
class:RNAString RNAString objects
class:RNAStringSet XStringSet objects
class:RNAStringSetList XStringSetList objects
class:RNA_WCP Weighted Clustered Positions (WCP) objects
class:SolexaQuality PhredQuality and SolexaQuality objects
class:TB_PDict PDict objects
class:Twobit PDict objects
class:WCP Weighted Clustered Positions (WCP) objects
class:XKeySortedData Data Dictionaries with XString-based Keys
class:XKeySortedDataList List of Data Dictionaries with XString-based Keys
class:XString BString objects
class:XStringPartialMatches XStringPartialMatches objects
class:XStringQuality PhredQuality and SolexaQuality objects
class:XStringSet XStringSet objects
class:XStringSetList XStringSetList objects
class:XStringViews The XStringViews class
codons DNA/RNA transcription and translation
codons-method DNA/RNA transcription and translation
coerce-method MIndex objects
coerce-method MaskedXString objects
coerce-method MultipleAlignment objects
coerce-method BString objects
coerce-method PhredQuality and SolexaQuality 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
complementedPalindromeArmLength Searching a sequence for palindromes or complemented palindromes
complementedPalindromeArmLength-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm Searching a sequence for palindromes or complemented palindromes
complementedPalindromeLeftArm-method Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm Searching a sequence for palindromes or complemented palindromes
complementedPalindromeRightArm-method Searching a sequence for palindromes or complemented palindromes
complementSeq Complementary sequence.
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
countbases Obtain the ATCG content of a gene
countIndex MIndex objects
countIndex-method MIndex objects
countPattern String searching functions
countPattern-method BOC\_SubjectString and BOC2\_SubjectString objects
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
countWCP A simple WCP matching function and related utilities
countWCP-method A simple WCP matching function 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 --

dataKey Data Dictionaries with XString-based Keys
dataKey-method Data Dictionaries with XString-based Keys
dataTable Data Dictionaries with XString-based Keys
dataTable-method Data Dictionaries with XString-based Keys
deletion InDel objects
deletion-method InDel objects
deletion-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
detail Show (display) detailed object content
detail-method MultipleAlignment objects
dim-method MultipleAlignment objects
dim-method Data Dictionaries with XString-based Keys
dimnames-method Data Dictionaries with XString-based Keys
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
dna2rna DNA/RNA transcription and translation
DNAKeySortedData Data Dictionaries with XString-based Keys
DNAKeySortedData-class Data Dictionaries with XString-based Keys
DNAKeySortedDataList List of Data Dictionaries with XString-based Keys
DNAKeySortedDataList-class List of Data Dictionaries with XString-based Keys
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
DNA_WCP Weighted Clustered Positions (WCP) objects
DNA_WCP-class Weighted Clustered Positions (WCP) objects
duplicated-method PDict objects
duplicated-method XStringSet objects

-- E --

elementLengths-method MIndex 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

-- F --

FASTA-io-legacy Legacy functions to read/write FASTA formatted files
fasta.info Read/write an XStringSet object from/to a file
FASTArecordsToCharacter Read/write an XStringSet object from/to a file
FASTArecordsToXStringViews Read/write an XStringSet object from/to a file
fastq.geometry Read/write an XStringSet object from/to a file
findComplementedPalindromes Searching a sequence for palindromes or complemented palindromes
findComplementedPalindromes-method Searching a sequence for palindromes or complemented palindromes
findPalindromes Searching a sequence for palindromes or complemented palindromes
findPalindromes-method Searching a sequence for palindromes or complemented palindromes

-- G --

gaps-method MaskedXString objects
GENETIC_CODE The Standard Genetic Code
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 --

InDel InDel objects
indel AlignedXStringSet and QualityAlignedXStringSet objects
InDel-class InDel objects
indel-method AlignedXStringSet and QualityAlignedXStringSet objects
indel-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
initialize-method BOC\_SubjectString and BOC2\_SubjectString 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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
intersect-method XStringSet objects
is.unsorted-method XStringSet objects
isMatching Low-level matching functions
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 AlignedXStringSet and QualityAlignedXStringSet objects
length-method MIndex objects
length-method MaskedXString objects
length-method PDict objects
length-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
length-method Data Dictionaries with XString-based Keys
length-method XStringSetList 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 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 BOC\_SubjectString and BOC2\_SubjectString objects
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
matchWCP A simple WCP matching function and related utilities
matchWCP-method A simple WCP matching function 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 Weighted Clustered Positions (WCP) objects
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 XStringSetList objects
names<--method MIndex objects
names<--method PDict objects
names<--method XStringSetList 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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
nchar-method BString objects
nchar-method XStringSet 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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary 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
nmismatchEndingAt Low-level matching functions
nmismatchStartingAt Low-level matching functions
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)
order-method XStringSet objects

-- P --

PairwiseAlignedFixedSubject PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubject-class PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubject-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubjectSummary PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedFixedSubjectSummary-class PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedXStringSet PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedXStringSet-class PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
PairwiseAlignedXStringSet-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
pairwiseAlignment Optimal Pairwise Alignment
pairwiseAlignment-method Optimal Pairwise Alignment
palindromeArmLength Searching a sequence for palindromes or complemented palindromes
palindromeArmLength-method Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm Searching a sequence for palindromes or complemented palindromes
palindromeLeftArm-method Searching a sequence for palindromes or complemented palindromes
palindromeRightArm Searching a sequence for palindromes or complemented palindromes
palindromeRightArm-method Searching a sequence for palindromes or complemented palindromes
PAM120 Scoring matrices
PAM250 Scoring matrices
PAM30 Scoring matrices
PAM40 Scoring matrices
PAM70 Scoring matrices
partitioning XStringSetList objects
partitioning-method XStringSetList objects
pattern XStringPartialMatches objects
pattern-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
pattern-method XStringPartialMatches objects
patternFrequency PDict objects
patternFrequency-method PDict 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 and SolexaQuality objects
PhredQuality-class PhredQuality and SolexaQuality 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
PWMscore 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 --

rank-method XStringSet objects
read.AAMultipleAlignment MultipleAlignment objects
read.AAStringSet Read/write an XStringSet object from/to a file
read.BStringSet Read/write an XStringSet object from/to a file
read.DNAMultipleAlignment MultipleAlignment objects
read.DNAStringSet Read/write an XStringSet object from/to a file
read.RNAMultipleAlignment MultipleAlignment objects
read.RNAStringSet Read/write an XStringSet object from/to a file
read.XStringViews Read/write an XStringSet object from/to a file
readFASTA Legacy functions to read/write FASTA formatted files
rep-method AlignedXStringSet and QualityAlignedXStringSet objects
rep-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
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
replaceLetterAtLoc Replacing letters in a sequence (or set of sequences) at some specified locations
revcompDNA Reverse Sequence
revcompRNA Reverse Sequence
reverse-method Sequence reversing and complementing
reverseComplement Sequence reversing and complementing
reverseComplement-method PWM creating, matching, and related utilities
reverseComplement-method Sequence reversing and complementing
reverseSeq Reverse Sequence
rna2dna DNA/RNA transcription and translation
RNAKeySortedData Data Dictionaries with XString-based Keys
RNAKeySortedData-class Data Dictionaries with XString-based Keys
RNAKeySortedDataList List of Data Dictionaries with XString-based Keys
RNAKeySortedDataList-class List of Data Dictionaries with XString-based Keys
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
RNA_WCP Weighted Clustered Positions (WCP) objects
RNA_WCP-class Weighted Clustered Positions (WCP) objects
rowmask MultipleAlignment objects
rowmask-method MultipleAlignment objects
rowmask<- MultipleAlignment objects
rowmask<--method MultipleAlignment objects
rownames-method MultipleAlignment objects
rownames<--method MultipleAlignment objects

-- S --

save.XStringSet Read/write an XStringSet object from/to a file
score-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
setdiff-method XStringSet objects
setequal-method XStringSet objects
show-method AlignedXStringSet and QualityAlignedXStringSet objects
show-method MIndex objects
show-method MaskedXString objects
show-method MultipleAlignment objects
show-method PDict objects
show-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
show-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
show-method Weighted Clustered Positions (WCP) objects
show-method BString objects
show-method XStringPartialMatches objects
show-method XStringSet objects
show-method XStringSetList objects
show-method The XStringViews class
SolexaQuality PhredQuality and SolexaQuality objects
SolexaQuality-class PhredQuality and SolexaQuality objects
sort-method XStringSet objects
srPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads
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
strrev Sequence reversing and complementing
subject-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary 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
subXString BString objects
summary-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary 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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
toString-method BString objects
toString-method XStringSet objects
toString-method The XStringViews class
transcribe DNA/RNA transcription and translation
translate DNA/RNA transcription and translation
translate-method DNA/RNA transcription and translation
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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
type-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects

-- U --

unaligned AlignedXStringSet and QualityAlignedXStringSet objects
unaligned-method AlignedXStringSet and QualityAlignedXStringSet objects
union-method XStringSet objects
unique-method XStringSet 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
unlist-method XStringSetList objects
unmasked MaskedXString objects
unmasked-method MaskedXString objects
unmasked-method MultipleAlignment objects
unsplit.list.of.XStringSet XStringSet 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 PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary 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 --

WCP Weighted Clustered Positions (WCP) objects
WCP-class Weighted Clustered Positions (WCP) objects
WCPscoreStartingAt A simple WCP matching function and related utilities
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
write.phylip MultipleAlignment objects
write.XStringSet Read/write an XStringSet object from/to a file
write.XStringViews Read/write an XStringSet object from/to a file
writeFASTA Legacy functions to read/write FASTA formatted files
wtPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads

-- X --

XKeySortedData Data Dictionaries with XString-based Keys
XKeySortedData-class Data Dictionaries with XString-based Keys
XKeySortedDataList List of Data Dictionaries with XString-based Keys
XKeySortedDataList-class List of Data Dictionaries with XString-based Keys
xsbasetype-method AlignedXStringSet and QualityAlignedXStringSet objects
xsbasetype-method MaskedXString objects
xsbasetype-method MultipleAlignment objects
xsbasetype-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
xsbasetype-method Weighted Clustered Positions (WCP) objects
xsbasetype-method Data Dictionaries with XString-based Keys
xsbasetype-method List of Data Dictionaries with XString-based Keys
xsbasetype-method BString objects
xsbasetype-method XStringSet objects
xsbasetype-method XStringSetList objects
xsbasetype-method The XStringViews class
xsbasetype<--method MaskedXString objects
xsbasetype<--method BString objects
xsbasetype<--method XStringSet objects
xsbasetype<--method XStringSetList objects
xsbasetype<--method The XStringViews class
xscat Concatenate sequences contained in XString, XStringSet and/or XStringViews objects
XString BString objects
XString-class BString objects
XStringPartialMatches-class XStringPartialMatches objects
XStringQuality PhredQuality and SolexaQuality objects
XStringQuality-class PhredQuality and SolexaQuality objects
XStringSet XStringSet objects
XStringSet-class XStringSet objects
XStringSet-io Read/write an XStringSet object from/to a file
XStringSetList XStringSetList objects
XStringSetList-class XStringSetList objects
XStringSetToFASTArecords Read/write an XStringSet object from/to a file
XStringViews Basic functions for creating or modifying XStringViews objects
XStringViews-class The XStringViews class
XStringViews-constructor Basic functions for creating or modifying XStringViews objects
XStringViews-method Basic functions for creating or modifying XStringViews objects

-- Y --

yeastSEQCHR1 An annotation data file for CHR1 in the yeastSEQ package

-- misc --

!=-method BString objects
!=-method The XStringViews class
%in%-method XStringSet objects
.inplaceReplaceLetterAt Replacing letters in a sequence (or set of sequences) at some specified locations
==-method BString objects
==-method The XStringViews class
[-method AlignedXStringSet and QualityAlignedXStringSet objects
[-method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
[-method QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects
[-method Data Dictionaries with XString-based Keys
[-method XStringPartialMatches objects
[<--method AlignedXStringSet and QualityAlignedXStringSet objects
[<--method PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects
[[-method MIndex objects
[[-method PDict objects
[[-method Data Dictionaries with XString-based Keys
[[-method XStringSetList objects
[[<--method XStringSetList objects