AAString |
AAString objects |
AAString-class |
AAString objects |
AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AA_ALPHABET |
AAString objects |
ACtree |
PDict objects |
ACtree-class |
PDict 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,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
aligned,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
alignScore |
(Deprecated) Needleman-Wunsch Global Alignment |
alphabet |
BString objects |
alphabet,AAString-method |
AAString objects |
alphabet,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
alphabet,BString-method |
BString objects |
alphabet,DNAString-method |
DNAString objects |
alphabet,MaskedXString-method |
MaskedXString objects |
alphabet,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
alphabet,RNAString-method |
RNAString objects |
alphabet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
alphabet,XStringViews-method |
The XStringViews class |
alphabetFrequency |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,DNAString-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,DNAStringSet-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,MaskedXString-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,RNAString-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,RNAStringSet-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,XString-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,XStringSet-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
alphabetFrequency,XStringViews-method |
Function to calculate the frequency of letters in a biological sequence and related functions |
AMINO_ACID_CODE |
The Single-Letter Amino Acid Code |
append,QualityScaledXStringSet,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
append,XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.character,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
as.character,MaskedXString-method |
MaskedXString objects |
as.character,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
as.character,XString-method |
BString objects |
as.character,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.character,XStringViews-method |
The XStringViews class |
as.complex,DNAString-method |
Turning a DNA sequence into a vector of complex numbers |
as.integer,PhredQuality-method |
PhredQuality and SolexaQuality objects |
as.integer,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
as.list,MTB_PDict-method |
PDict objects |
as.matrix,ACtree-method |
PDict objects |
as.matrix,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
as.matrix,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.matrix,XStringViews-method |
The XStringViews class |
as.numeric,PhredQuality-method |
PhredQuality and SolexaQuality objects |
as.numeric,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
cDNA |
DNA/RNA transcription and translation |
CharacterToFASTArecords |
Read/write an XStringSet or XStringViews object from/to a file |
chartr |
Translating letters of a sequence |
chartr,MaskedXString-method |
Translating letters of a sequence |
chartr,XString-method |
Translating letters of a sequence |
chartr,XStringSet-method |
Translating letters of a sequence |
chartr,XStringViews-method |
Translating letters of a sequence |
class:AAString |
AAString objects |
class:AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:ACtree |
PDict objects |
class:ACtree2 |
PDict objects |
class:AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
class:BOC2_SubjectString |
BOC_SubjectString and BOC2_SubjectString objects |
class:BOC_SubjectString |
BOC_SubjectString and BOC2_SubjectString objects |
class:BString |
BString objects |
class:BStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:ByPos_MIndex |
MIndex objects |
class:DNAString |
DNAString objects |
class:DNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet 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:PairwiseAlignedFixedSubject |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
class:PairwiseAlignedFixedSubjectSummary |
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:RNAString |
RNAString objects |
class:RNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:SolexaQuality |
PhredQuality and SolexaQuality objects |
class:TB_PDict |
PDict objects |
class:Twobit |
PDict objects |
class:XString |
BString objects |
class:XStringPartialMatches |
XStringPartialMatches objects |
class:XStringQuality |
PhredQuality and SolexaQuality objects |
class:XStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:XStringViews |
The XStringViews class |
codons |
DNA/RNA transcription and translation |
codons,DNAString-method |
DNA/RNA transcription and translation |
codons,MaskedDNAString-method |
DNA/RNA transcription and translation |
codons,MaskedRNAString-method |
DNA/RNA transcription and translation |
codons,RNAString-method |
DNA/RNA transcription and translation |
coerce,AAString,MaskedAAString-method |
MaskedXString objects |
coerce,BString,MaskedBString-method |
MaskedXString objects |
coerce,BString,PhredQuality-method |
PhredQuality and SolexaQuality objects |
coerce,BString,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
coerce,BStringSet,PhredQuality-method |
PhredQuality and SolexaQuality objects |
coerce,BStringSet,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
coerce,character,PhredQuality-method |
PhredQuality and SolexaQuality objects |
coerce,character,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
coerce,DNAString,MaskedDNAString-method |
MaskedXString objects |
coerce,integer,PhredQuality-method |
PhredQuality and SolexaQuality objects |
coerce,integer,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
coerce,MaskedAAString,AAString-method |
MaskedXString objects |
coerce,MaskedBString,BString-method |
MaskedXString objects |
coerce,MaskedDNAString,DNAString-method |
MaskedXString objects |
coerce,MaskedRNAString,RNAString-method |
MaskedXString objects |
coerce,MaskedXString,MaskCollection-method |
MaskedXString objects |
coerce,MaskedXString,NormalIRanges-method |
MaskedXString objects |
coerce,MaskedXString,XStringViews-method |
MaskedXString objects |
coerce,numeric,PhredQuality-method |
PhredQuality and SolexaQuality objects |
coerce,numeric,SolexaQuality-method |
PhredQuality and SolexaQuality objects |
coerce,PhredQuality,integer-method |
PhredQuality and SolexaQuality objects |
coerce,PhredQuality,numeric-method |
PhredQuality and SolexaQuality objects |
coerce,RNAString,MaskedRNAString-method |
MaskedXString objects |
coerce,SolexaQuality,integer-method |
PhredQuality and SolexaQuality objects |
coerce,SolexaQuality,numeric-method |
PhredQuality and SolexaQuality objects |
coerce,XStringSet,AAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
coerce,XStringSet,BStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
coerce,XStringSet,DNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
coerce,XStringSet,RNAStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
compareStrings |
Utility functions related to sequence alignment |
compareStrings,AlignedXStringSet,AlignedXStringSet-method |
Utility functions related to sequence alignment |
compareStrings,character,character-method |
Utility functions related to sequence alignment |
compareStrings,PairwiseAlignedFixedSubject,missing-method |
Utility functions related to sequence alignment |
compareStrings,XString,XString-method |
Utility functions related to sequence alignment |
compareStrings,XStringSet,XStringSet-method |
Utility functions related to sequence alignment |
complement |
Sequence reversing and complementing |
complement,DNAString-method |
Sequence reversing and complementing |
complement,DNAStringSet-method |
Sequence reversing and complementing |
complement,MaskedDNAString-method |
Sequence reversing and complementing |
complement,MaskedRNAString-method |
Sequence reversing and complementing |
complement,RNAString-method |
Sequence reversing and complementing |
complement,RNAStringSet-method |
Sequence reversing and complementing |
complement,XStringViews-method |
Sequence reversing and complementing |
complementedPalindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeArmLength,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeArmLength,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeLeftArm,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeLeftArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeRightArm,DNAString-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeRightArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
consensusMatrix |
Utility functions related to sequence alignment |
consensusMatrix,character-method |
Utility functions related to sequence alignment |
consensusMatrix,list-method |
Utility functions related to sequence alignment |
consensusMatrix,matrix-method |
Utility functions related to sequence alignment |
consensusMatrix,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
consensusMatrix,XStringSet-method |
Utility functions related to sequence alignment |
consensusMatrix,XStringViews-method |
Utility functions related to sequence alignment |
consensusString |
Utility functions related to sequence alignment |
consensusString,ANY-method |
Utility functions related to sequence alignment |
consmat |
Utility functions related to sequence alignment |
consmat,ANY-method |
Utility functions related to sequence alignment |
countIndex |
MIndex objects |
countIndex,ByPos_MIndex-method |
MIndex objects |
countIndex,MIndex-method |
MIndex objects |
countPattern |
String searching functions |
countPattern,BOC2_SubjectString-method |
BOC_SubjectString and BOC2_SubjectString objects |
countPattern,character-method |
String searching functions |
countPattern,MaskedXString-method |
String searching functions |
countPattern,XString-method |
String searching functions |
countPattern,XStringSet-method |
String searching functions |
countPattern,XStringViews-method |
String searching functions |
countPDict |
Searching a sequence for patterns stored in a preprocessed dictionary |
countPDict,MaskedXString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
countPDict,XString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
countPDict,XStringSet-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
countPDict,XStringViews-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
countPWM |
A simple PWM matching function and related utilities |
coverage,AlignedXStringSet-method |
Utility functions related to sequence alignment |
coverage,MaskedXString-method |
Utility functions related to pattern matching |
coverage,MIndex-method |
Utility functions related to pattern matching |
coverage,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
coverage,PairwiseAlignedFixedSubjectSummary-method |
Utility functions related to sequence alignment |
coverage,XStringViews-method |
Utility functions related to pattern matching |
lcprefix |
Longest Common Prefix/Suffix/Substring searching functions |
lcprefix,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcprefix,character,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcprefix,XString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcprefix,XString,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsubstr |
Longest Common Prefix/Suffix/Substring searching functions |
lcsubstr,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsubstr,character,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsubstr,XString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsubstr,XString,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsuffix |
Longest Common Prefix/Suffix/Substring searching functions |
lcsuffix,character,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsuffix,character,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsuffix,XString,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
lcsuffix,XString,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
length,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
length,MaskedXString-method |
MaskedXString objects |
length,MIndex-method |
MIndex objects |
length,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
length,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
length,PDict-method |
PDict objects |
length,PDict3Parts-method |
PDict objects |
length,PreprocessedTB-method |
PDict objects |
length,XString-method |
BString objects |
length,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
letter |
Subsetting a string |
letter,character-method |
Subsetting a string |
letter,MaskedXString-method |
Subsetting a string |
letter,XString-method |
Subsetting a string |
letter,XStringViews-method |
Subsetting a string |
mask |
Masking by content (or by position) |
MaskedAAString |
MaskedXString objects |
MaskedAAString-class |
MaskedXString objects |
MaskedBString |
MaskedXString objects |
MaskedBString-class |
MaskedXString objects |
MaskedDNAString |
MaskedXString objects |
MaskedDNAString-class |
MaskedXString objects |
maskedratio,MaskedXString-method |
MaskedXString objects |
MaskedRNAString |
MaskedXString objects |
MaskedRNAString-class |
MaskedXString objects |
maskedwidth,MaskedXString-method |
MaskedXString objects |
MaskedXString |
MaskedXString objects |
MaskedXString-class |
MaskedXString objects |
maskMotif |
Masking by content (or by position) |
maskMotif,MaskedXString,character-method |
Masking by content (or by position) |
maskMotif,MaskedXString,XString-method |
Masking by content (or by position) |
maskMotif,XString,ANY-method |
Masking by content (or by position) |
masks |
MaskedXString objects |
masks,MaskedXString-method |
MaskedXString objects |
masks,XString-method |
MaskedXString objects |
masks<-,MaskedXString,MaskCollection-method |
MaskedXString objects |
masks<-,MaskedXString,NULL-method |
MaskedXString objects |
masks<-,XString,ANY-method |
MaskedXString objects |
masks<-,XString,NULL-method |
MaskedXString objects |
match-utils |
Utility functions related to pattern matching |
matchDNAPattern |
String searching functions |
matchLRPatterns |
Find paired matches in a sequence |
matchLRPatterns,MaskedXString-method |
Find paired matches in a sequence |
matchLRPatterns,XString-method |
Find paired matches in a sequence |
matchLRPatterns,XStringViews-method |
Find paired matches in a sequence |
matchPattern |
String searching functions |
matchPattern,BOC2_SubjectString-method |
BOC_SubjectString and BOC2_SubjectString objects |
matchPattern,BOC_SubjectString-method |
BOC_SubjectString and BOC2_SubjectString objects |
matchPattern,character-method |
String searching functions |
matchPattern,MaskedXString-method |
String searching functions |
matchPattern,XString-method |
String searching functions |
matchPattern,XStringSet-method |
String searching functions |
matchPattern,XStringViews-method |
String searching functions |
matchPDict |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict,MaskedXString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict,XString-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict,XStringSet-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict,XStringViews-method |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict-exact |
Searching a sequence for patterns stored in a preprocessed dictionary |
matchPDict-inexact |
Inexact matching with matchPDict()/countPDict()/whichPDict() |
matchProbePair |
Find "theoretical amplicons" mapped to a probe pair |
matchProbePair,DNAString-method |
Find "theoretical amplicons" mapped to a probe pair |
matchProbePair,MaskedDNAString-method |
Find "theoretical amplicons" mapped to a probe pair |
matchProbePair,XStringViews-method |
Find "theoretical amplicons" mapped to a probe pair |
matchPWM |
A simple PWM matching function and related utilities |
maxScore |
A simple PWM matching function and related utilities |
maxWeights |
A simple PWM matching function and related utilities |
mergeIUPACLetters |
The IUPAC Extended Genetic Alphabet |
MIndex |
MIndex objects |
MIndex-class |
MIndex objects |
mismatch |
Utility functions related to pattern matching |
mismatch,AlignedXStringSet,missing-method |
Utility functions related to sequence alignment |
mismatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
mismatchSummary |
Utility functions related to sequence alignment |
mismatchSummary,AlignedXStringSet-method |
Utility functions related to sequence alignment |
mismatchSummary,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
mismatchSummary,PairwiseAlignedFixedSubjectSummary-method |
Utility functions related to sequence alignment |
mismatchSummary,QualityAlignedXStringSet-method |
Utility functions related to sequence alignment |
mismatchTable |
Utility functions related to sequence alignment |
mismatchTable,AlignedXStringSet-method |
Utility functions related to sequence alignment |
mismatchTable,PairwiseAlignedFixedSubject-method |
Utility functions related to sequence alignment |
mismatchTable,QualityAlignedXStringSet-method |
Utility functions related to sequence alignment |
mkAllStrings |
Function to calculate the frequency of letters in a biological sequence and related functions |
MTB_PDict |
PDict objects |
MTB_PDict-class |
PDict objects |
names,MIndex-method |
MIndex objects |
names,PDict-method |
PDict objects |
names,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
names<-,MIndex-method |
MIndex objects |
names<-,PDict-method |
PDict objects |
names<-,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
narrow,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
narrow,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
nchar,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
nchar,MaskedXString-method |
MaskedXString objects |
nchar,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
nchar,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
nchar,XString-method |
BString objects |
nchar,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
nchar,XStringViews-method |
The XStringViews class |
neditAt |
Utility functions related to pattern matching |
neditEndingAt |
Utility functions related to pattern matching |
neditEndingAt,character-method |
Utility functions related to pattern matching |
neditEndingAt,XString-method |
Utility functions related to pattern matching |
neditStartingAt |
Utility functions related to pattern matching |
neditStartingAt,character-method |
Utility functions related to pattern matching |
neditStartingAt,XString-method |
Utility functions related to pattern matching |
needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
needwunsQS,character,character-method |
(Deprecated) Needleman-Wunsch Global Alignment |
needwunsQS,character,XString-method |
(Deprecated) Needleman-Wunsch Global Alignment |
needwunsQS,XString,character-method |
(Deprecated) Needleman-Wunsch Global Alignment |
needwunsQS,XString,XString-method |
(Deprecated) Needleman-Wunsch Global Alignment |
nindel |
AlignedXStringSet and QualityAlignedXStringSet objects |
nindel,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
nindel,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
nindel,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
nmatch |
Utility functions related to pattern matching |
nmatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
nmatch,PairwiseAlignedFixedSubject,missing-method |
Utility functions related to sequence alignment |
nmatch,PairwiseAlignedFixedSubjectSummary,missing-method |
Utility functions related to sequence alignment |
nmismatch |
Utility functions related to pattern matching |
nmismatch,AlignedXStringSet,missing-method |
Utility functions related to sequence alignment |
nmismatch,ANY,XStringViews-method |
Utility functions related to pattern matching |
nmismatch,PairwiseAlignedFixedSubject,missing-method |
Utility functions related to sequence alignment |
nmismatch,PairwiseAlignedFixedSubjectSummary,missing-method |
Utility functions related to sequence alignment |
nmismatchEndingAt |
Utility functions related to pattern matching |
nmismatchStartingAt |
Utility functions related to pattern matching |
nucleotideSubstitutionMatrix |
Scoring matrices |
PairwiseAlignedFixedSubject |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubject-class |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubjectSummary |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubjectSummary-class |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
pairwiseAlignment |
Optimal Pairwise Alignment |
pairwiseAlignment,character,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,character,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,character,XString-method |
Optimal Pairwise Alignment |
pairwiseAlignment,character,XStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,QualityScaledXStringSet,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,QualityScaledXStringSet,XString-method |
Optimal Pairwise Alignment |
pairwiseAlignment,QualityScaledXStringSet,XStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,XString-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,XStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XStringSet,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XStringSet,QualityScaledXStringSet-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XStringSet,XString-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XStringSet,XStringSet-method |
Optimal Pairwise Alignment |
palindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
palindromeArmLength,XString-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeArmLength,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
palindromeLeftArm,XString-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeLeftArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
palindromeRightArm,XString-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeRightArm,XStringViews-method |
Searching a sequence for palindromes or complemented palindromes |
PAM120 |
Scoring matrices |
PAM250 |
Scoring matrices |
PAM30 |
Scoring matrices |
PAM40 |
Scoring matrices |
PAM70 |
Scoring matrices |
pattern |
XStringPartialMatches objects |
pattern,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
pattern,XStringPartialMatches-method |
XStringPartialMatches objects |
patternFrequency |
PDict objects |
patternFrequency,PDict-method |
PDict objects |
PDict |
PDict objects |
PDict,AsIs-method |
PDict objects |
PDict,character-method |
PDict objects |
PDict,DNAStringSet-method |
PDict objects |
PDict,XStringViews-method |
PDict objects |
PDict-class |
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,PairwiseAlignedFixedSubject-method |
Percent Sequence Identity |
pmatchPattern |
Longest Common Prefix/Suffix/Substring searching functions |
pmatchPattern,character-method |
Longest Common Prefix/Suffix/Substring searching functions |
pmatchPattern,XString-method |
Longest Common Prefix/Suffix/Substring searching functions |
pmatchPattern,XStringViews-method |
Longest Common Prefix/Suffix/Substring searching functions |
PreprocessedTB |
PDict objects |
PreprocessedTB-class |
PDict objects |
print.needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
PWMscore |
A simple PWM matching function and related utilities |
quality |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
quality,QualityScaledXStringSet-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 |
read.AAStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.BStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.BStringViews |
Read/write an XStringSet or XStringViews object from/to a file |
read.DNAStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.RNAStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.XStringViews |
Read/write an XStringSet or XStringViews object from/to a file |
readFASTA |
Functions to read/write FASTA formatted files |
reduce,MaskedXString-method |
MaskedXString objects |
rep,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
rep,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
rep,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
replaceLetterAt |
Replacing letters in a sequence at some specified locations |
replaceLetterAt,DNAString-method |
Replacing letters in a sequence at some specified locations |
replaceLetterAtLoc |
Replacing letters in a sequence at some specified locations |
reverse,MaskedXString-method |
Sequence reversing and complementing |
reverse,XString-method |
Sequence reversing and complementing |
reverse,XStringSet-method |
Sequence reversing and complementing |
reverse,XStringViews-method |
Sequence reversing and complementing |
reverseComplement |
Sequence reversing and complementing |
reverseComplement,DNAString-method |
Sequence reversing and complementing |
reverseComplement,DNAStringSet-method |
Sequence reversing and complementing |
reverseComplement,MaskedDNAString-method |
Sequence reversing and complementing |
reverseComplement,MaskedRNAString-method |
Sequence reversing and complementing |
reverseComplement,matrix-method |
A simple PWM matching function and related utilities |
reverseComplement,RNAString-method |
Sequence reversing and complementing |
reverseComplement,RNAStringSet-method |
Sequence reversing and complementing |
reverseComplement,XStringViews-method |
Sequence reversing and complementing |
rna2dna |
DNA/RNA transcription and translation |
RNAString |
RNAString objects |
RNAString-class |
RNAString objects |
RNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNA_ALPHABET |
RNAString objects |
RNA_BASES |
RNAString objects |
RNA_GENETIC_CODE |
The Standard Genetic Code |
score |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
score,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
score,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
show,ACtree-method |
PDict objects |
show,ACtree2-method |
PDict objects |
show,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
show,ByPos_MIndex-method |
MIndex objects |
show,MaskedXString-method |
MaskedXString objects |
show,MTB_PDict-method |
PDict objects |
show,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
show,PairwiseAlignedFixedSubjectSummary-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
show,QualityScaledXStringSet-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
show,TB_PDict-method |
PDict objects |
show,Twobit-method |
PDict objects |
show,XString-method |
BString objects |
show,XStringPartialMatches-method |
XStringPartialMatches objects |
show,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
show,XStringViews-method |
The XStringViews class |
SolexaQuality |
PhredQuality and SolexaQuality objects |
SolexaQuality-class |
PhredQuality and SolexaQuality objects |
sort,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
srPhiX174 |
Versions of bacteriophage phiX174 complete genome and sample short reads |
start,AlignedXStringSet-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
startIndex |
MIndex objects |
startIndex,ByPos_MIndex-method |
MIndex objects |
stringDist |
String Distance/Alignment Score Matrix |
stringDist,character-method |
String Distance/Alignment Score Matrix |
stringDist,QualityScaledXStringSet-method |
String Distance/Alignment Score Matrix |
stringDist,XStringSet-method |
String Distance/Alignment Score Matrix |
strrev |
Function to calculate the frequency of letters in a biological sequence and related functions |
subBString |
Fast substring extraction |
subject,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |
subpatterns |
XStringPartialMatches objects |
subpatterns,XStringPartialMatches-method |
XStringPartialMatches objects |
subseq,MaskedXString-method |
MaskedXString objects |
substitution.matrices |
Scoring matrices |
substr |
Fast substring extraction |
substr,MaskedXString-method |
Fast substring extraction |
substr,XString-method |
Fast substring extraction |
substring |
Fast substring extraction |
substring,MaskedXString-method |
Fast substring extraction |
substring,XString-method |
Fast substring extraction |
subXString |
Fast substring extraction |
summary,PairwiseAlignedFixedSubject-method |
PairwiseAlignedFixedSubject and PairwiseAlignedFixedSubjectSummary objects |