AAString |
AAString objects |
AAString-class |
AAString objects |
AAStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringList,ANY-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringList,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringList,vector-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringList,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringList-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AAStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
AA_ALPHABET |
AAString objects |
active |
MaskCollection objects |
active,MaskCollection-method |
MaskCollection objects |
active<-,MaskCollection-method |
MaskCollection objects |
ACtree |
PDict objects |
ACtree-class |
PDict objects |
adjacentViews |
Basic functions for creating or modifying XStringViews objects |
align1 |
XStringAlign objects |
align1,XStringAlign-method |
XStringAlign objects |
align2 |
XStringAlign objects |
align2,XStringAlign-method |
XStringAlign objects |
alignScore |
(Deprecated) Needleman-Wunsch Global Alignment |
alphabet |
BString objects |
alphabet,AAString-method |
AAString objects |
alphabet,BString-method |
BString objects |
alphabet,DNAString-method |
DNAString objects |
alphabet,MaskedXString-method |
MaskedXString objects |
alphabet,RNAString-method |
RNAString objects |
alphabet,XStringAlign-method |
XStringAlign objects |
alphabet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
alphabet,XStringViews-method |
The XStringViews class |
alphabetFrequency |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,DNAString-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,DNAStringSet-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,MaskedXString-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,RNAString-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,RNAStringSet-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,XString-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,XStringSet-method |
Functions to calculate the frequency of letters in a biological sequence |
alphabetFrequency,XStringViews-method |
Functions to calculate the frequency of letters in a biological sequence |
AMINO_ACID_CODE |
The Single-Letter Amino Acid Code |
append,MaskCollection-method |
MaskCollection objects |
as.character,MaskedXString-method |
MaskedXString objects |
as.character,XString-method |
BString objects |
as.character,XStringAlign-method |
XStringAlign objects |
as.character,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.character,XStringViews-method |
The XStringViews class |
as.complex,DNAString-method |
Converting a DNAString to a vector of complexes |
as.data.frame,IRanges-method |
IRanges and NormalIRanges objects |
as.list,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.list,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
as.list,XStringViews-method |
The XStringViews class |
as.matrix,ACtree-method |
PDict objects |
as.matrix,IRanges-method |
IRanges and NormalIRanges objects |
as.matrix,XStringViews-method |
The XStringViews class |
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 |
BStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringList,ANY-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringList,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringList,vector-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringList,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringList-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
BStringViews |
Basic functions for creating or modifying XStringViews objects |
BStringViews,ANY-method |
Basic functions for creating or modifying XStringViews objects |
BStringViews,file-method |
Basic functions for creating or modifying XStringViews objects |
BStringViews,XString-method |
Basic functions for creating or modifying XStringViews objects |
BStringViews,XStringViews-method |
Basic functions for creating or modifying XStringViews objects |
ByName_MIndex-class |
Searching a sequence for patterns stored in a dictionary |
ByPos_MIndex-class |
Searching a sequence for patterns stored in a dictionary |
cDNA |
Sequence reversing and complementing |
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:AAStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:AAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:ACtree |
PDict objects |
class:BOC2_SubjectString |
BOC_SubjectString and BOC2_SubjectString objects |
class:BOC_SubjectString |
BOC_SubjectString and BOC2_SubjectString objects |
class:BString |
BString objects |
class:BStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:BStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:ByName_MIndex |
Searching a sequence for patterns stored in a dictionary |
class:ByPos_MIndex |
Searching a sequence for patterns stored in a dictionary |
class:CWdna_PDict |
PDict objects |
class:DNAString |
DNAString objects |
class:DNAStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:DNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:Dups |
PDict objects |
class:IRanges |
IRanges and NormalIRanges objects |
class:LockedIRanges |
IRanges and NormalIRanges objects |
class:MaskCollection |
MaskCollection objects |
class:MaskedAAString |
MaskedXString objects |
class:MaskedBString |
MaskedXString objects |
class:MaskedDNAString |
MaskedXString objects |
class:MaskedRNAString |
MaskedXString objects |
class:MaskedXString |
MaskedXString objects |
class:MIndex |
Searching a sequence for patterns stored in a dictionary |
class:NormalIRanges |
IRanges and NormalIRanges objects |
class:PDict |
PDict objects |
class:RNAString |
RNAString objects |
class:RNAStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:RNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:TBdna_PDict |
PDict objects |
class:UnlockedIRanges |
IRanges and NormalIRanges objects |
class:Views |
IRanges and NormalIRanges objects |
class:XString |
BString objects |
class:XStringAlign |
XStringAlign objects |
class:XStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:XStringPartialMatches |
XStringPartialMatches objects |
class:XStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
class:XStringViews |
The XStringViews class |
coerce,AAString,MaskedAAString-method |
MaskedXString objects |
coerce,BString,MaskedBString-method |
MaskedXString objects |
coerce,DNAString,MaskedDNAString-method |
MaskedXString objects |
coerce,IRanges,NormalIRanges-method |
IRanges and NormalIRanges objects |
coerce,LockedIRanges,NormalIRanges-method |
IRanges and NormalIRanges objects |
coerce,MaskCollection,NormalIRanges-method |
MaskCollection 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,RNAString,MaskedRNAString-method |
MaskedXString objects |
coerce,UnlockedIRanges,NormalIRanges-method |
IRanges and NormalIRanges objects |
coerce,Views,NormalIRanges-method |
IRanges and NormalIRanges objects |
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 |
consmat |
Utility functions related to sequence alignment |
consmat,character-method |
Utility functions related to sequence alignment |
consmat,list-method |
Utility functions related to sequence alignment |
consmat,matrix-method |
Utility functions related to sequence alignment |
consmat,XStringAlign-method |
Utility functions related to sequence alignment |
consmat,XStringSet-method |
Utility functions related to sequence alignment |
consmat,XStringViews-method |
Utility functions related to sequence alignment |
countIndex |
Searching a sequence for patterns stored in a dictionary |
countIndex,ByName_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
countIndex,ByPos_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
countIndex,MIndex-method |
Searching a sequence for patterns stored in a dictionary |
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,XStringViews-method |
String searching functions |
countPDict |
Searching a sequence for patterns stored in a dictionary |
countPDict,MaskedXString-method |
Searching a sequence for patterns stored in a dictionary |
countPDict,XString-method |
Searching a sequence for patterns stored in a dictionary |
countPDict,XStringViews-method |
Searching a sequence for patterns stored in a dictionary |
countPWM |
A simple PWM matching function and related utilities |
coverage |
Utility functions related to pattern matching |
coverage,IRanges-method |
Utility functions related to pattern matching |
coverage,MaskCollection-method |
Utility functions related to pattern matching |
coverage,MaskedXString-method |
Utility functions related to pattern matching |
coverage,MIndex-method |
Utility functions related to pattern matching |
coverage,XStringViews-method |
Utility functions related to pattern matching |
CWdna_PDict |
PDict objects |
CWdna_PDict-class |
PDict objects |
initialize,AAStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
initialize,ACtree-method |
PDict objects |
initialize,BOC2_SubjectString-method |
BOC_SubjectString and BOC2_SubjectString objects |
initialize,BOC_SubjectString-method |
BOC_SubjectString and BOC2_SubjectString objects |
initialize,BStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
initialize,CWdna_PDict-method |
PDict objects |
initialize,DNAStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
initialize,IRanges-method |
IRanges and NormalIRanges objects |
initialize,NormalIRanges-method |
IRanges and NormalIRanges objects |
initialize,RNAStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
initialize,TBdna_PDict-method |
PDict objects |
initialize,Views-method |
IRanges and NormalIRanges objects |
initialize,XStringAlign-method |
XStringAlign objects |
initialize,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
initialize,XStringViews-method |
The XStringViews class |
injectHardMask |
Injecting a hard mask in a sequence |
injectHardMask,MaskedXString-method |
Injecting a hard mask in a sequence |
injectHardMask,XStringViews-method |
Injecting a hard mask in a sequence |
intToAdjacentRanges |
IRanges utility functions |
intToRanges |
IRanges utility functions |
IRanges |
IRanges and NormalIRanges objects |
IRanges-class |
IRanges and NormalIRanges objects |
IRanges-utils |
IRanges utility functions |
isEmpty |
IRanges and NormalIRanges objects |
isEmpty,IRanges-method |
IRanges and NormalIRanges objects |
isEmpty,MaskCollection-method |
MaskCollection objects |
isEmpty,NormalIRanges-method |
IRanges and NormalIRanges objects |
isMatching |
Utility functions related to pattern matching |
isMatching,character-method |
Utility functions related to pattern matching |
isMatching,XString-method |
Utility functions related to pattern matching |
isNormal |
IRanges and NormalIRanges objects |
isNormal,IRanges-method |
IRanges and NormalIRanges objects |
IUPAC_CODE_MAP |
The IUPAC Extended Genetic Alphabet |
last |
IRanges and NormalIRanges objects |
last,IRanges-method |
IRanges and NormalIRanges objects |
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,ACtree-method |
PDict objects |
length,ByName_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
length,ByPos_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
length,CWdna_PDict-method |
PDict objects |
length,Dups-method |
PDict objects |
length,IRanges-method |
IRanges and NormalIRanges objects |
length,MaskCollection-method |
MaskCollection objects |
length,MaskedXString-method |
MaskedXString objects |
length,XString-method |
BString objects |
length,XStringAlign-method |
XStringAlign objects |
length,XStringList-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 |
LockedIRanges |
IRanges and NormalIRanges objects |
LockedIRanges-class |
IRanges and NormalIRanges objects |
Mask |
MaskCollection objects |
mask |
Masking by content (or by position) |
MaskCollection |
MaskCollection objects |
MaskCollection-class |
MaskCollection objects |
MaskedAAString |
MaskedXString objects |
MaskedAAString-class |
MaskedXString objects |
MaskedBString |
MaskedXString objects |
MaskedBString-class |
MaskedXString objects |
MaskedDNAString |
MaskedXString objects |
MaskedDNAString-class |
MaskedXString objects |
maskedratio |
MaskCollection objects |
maskedratio,MaskCollection-method |
MaskCollection objects |
maskedratio,MaskedXString-method |
MaskedXString objects |
MaskedRNAString |
MaskedXString objects |
MaskedRNAString-class |
MaskedXString objects |
maskedwidth |
MaskCollection objects |
maskedwidth,MaskCollection-method |
MaskCollection 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 patterns defined by a left and a right part in a sequence |
matchLRPatterns,MaskedXString-method |
Find patterns defined by a left and a right part in a sequence |
matchLRPatterns,XString-method |
Find patterns defined by a left and a right part in a sequence |
matchLRPatterns,XStringViews-method |
Find patterns defined by a left and a right part 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,XStringViews-method |
String searching functions |
matchPDict |
Searching a sequence for patterns stored in a dictionary |
matchPDict,MaskedXString-method |
Searching a sequence for patterns stored in a dictionary |
matchPDict,XString-method |
Searching a sequence for patterns stored in a dictionary |
matchPDict,XStringViews-method |
Searching a sequence for patterns stored in a dictionary |
matchPDict-exact |
Searching a sequence for patterns stored in a dictionary |
matchPDict-inexact |
Inexact matching with matchPDict() |
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 |
max,MaskCollection-method |
MaskCollection objects |
max,NormalIRanges-method |
IRanges and NormalIRanges objects |
maxScore |
A simple PWM matching function and related utilities |
maxWeights |
A simple PWM matching function and related utilities |
mergeIUPACLetters |
The IUPAC Extended Genetic Alphabet |
min,MaskCollection-method |
MaskCollection objects |
min,NormalIRanges-method |
IRanges and NormalIRanges objects |
MIndex |
Searching a sequence for patterns stored in a dictionary |
MIndex-class |
Searching a sequence for patterns stored in a dictionary |
mismatch |
Utility functions related to pattern matching |
mismatch,XStringViews-method |
Utility functions related to pattern matching |
mkAllStrings |
Functions to calculate the frequency of letters in a biological sequence |
names,ByName_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
names,ByPos_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
names,CWdna_PDict-method |
PDict objects |
names,IRanges-method |
IRanges and NormalIRanges objects |
names,MaskCollection-method |
MaskCollection objects |
names,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
names<-,IRanges-method |
IRanges and NormalIRanges objects |
names<-,MaskCollection-method |
MaskCollection objects |
names<-,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
narrow |
IRanges utility functions |
narrow,IRanges-method |
IRanges utility functions |
narrow,MaskCollection-method |
MaskCollection objects |
narrow,NormalIRanges-method |
IRanges utility functions |
narrow,numeric-method |
IRanges utility functions |
narrow,XStringViews-method |
Basic functions for creating or modifying XStringViews objects |
nchar,MaskedXString-method |
MaskedXString objects |
nchar,XString-method |
BString objects |
nchar,XStringAlign-method |
XStringAlign objects |
nchar,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
nchar,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
nchar,XStringViews-method |
The XStringViews class |
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 |
nir_list |
MaskCollection objects |
nir_list,MaskCollection-method |
MaskCollection objects |
nmismatchEndingAt |
Utility functions related to pattern matching |
nmismatchEndingAt,character-method |
Utility functions related to pattern matching |
nmismatchEndingAt,XString-method |
Utility functions related to pattern matching |
nmismatchStartingAt |
Utility functions related to pattern matching |
nmismatchStartingAt,character-method |
Utility functions related to pattern matching |
nmismatchStartingAt,XString-method |
Utility functions related to pattern matching |
NormalIRanges |
IRanges and NormalIRanges objects |
NormalIRanges-class |
IRanges and NormalIRanges objects |
pairwiseAlignment |
Optimal Pairwise Alignment |
pairwiseAlignment,character,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,character,XString-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,character-method |
Optimal Pairwise Alignment |
pairwiseAlignment,XString,XString-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,XStringPartialMatches-method |
XStringPartialMatches objects |
patternFrequency |
PDict objects |
patternFrequency,CWdna_PDict-method |
PDict objects |
patternFrequency,TBdna_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 |
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 |
print.needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
PWMscore |
A simple PWM matching function and related utilities |
read.AAStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.agpMask |
Read a mask from 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.gapMask |
Read a mask from a file |
read.liftMask |
Read a mask from a file |
read.Mask |
Read a mask from a file |
read.rmMask |
Read a mask from a file |
read.RNAStringSet |
Read/write an XStringSet or XStringViews object from/to a file |
read.trfMask |
Read a mask from a file |
read.XStringViews |
Read/write an XStringSet or XStringViews object from/to a file |
readFASTA |
Functions to read/write FASTA formatted files |
reduce |
IRanges utility functions |
reduce,IRanges-method |
IRanges utility functions |
reduce,MaskCollection-method |
MaskCollection objects |
reduce,MaskedXString-method |
MaskedXString objects |
replaceLetterAtLoc |
Replacing letters in a sequence at some specified locations |
replaceLetterAtLoc,DNAString-method |
Replacing letters in a sequence at some specified locations |
restrict |
IRanges utility functions |
restrict,IRanges-method |
IRanges utility functions |
restrict,XStringViews-method |
Basic functions for creating or modifying XStringViews objects |
reverse |
Sequence reversing and complementing |
reverse,IRanges-method |
Sequence reversing and complementing |
reverse,MaskCollection-method |
Sequence reversing and complementing |
reverse,MaskedXString-method |
Sequence reversing and complementing |
reverse,NormalIRanges-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 |
Sequence reversing and complementing |
RNAString |
RNAString objects |
RNAString-class |
RNAString objects |
RNAStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringList,ANY-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringList,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringList,vector-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringList,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringList-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNAStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
RNA_ALPHABET |
RNAString objects |
score |
XStringAlign objects |
score,XStringAlign-method |
XStringAlign objects |
shift |
IRanges utility functions |
shift,IRanges-method |
IRanges utility functions |
show,ACtree-method |
PDict objects |
show,ByName_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
show,ByPos_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
show,CWdna_PDict-method |
PDict objects |
show,IRanges-method |
IRanges and NormalIRanges objects |
show,MaskCollection-method |
MaskCollection objects |
show,MaskedXString-method |
MaskedXString objects |
show,TBdna_PDict-method |
PDict objects |
show,XString-method |
BString objects |
show,XStringAlign-method |
XStringAlign objects |
show,XStringList-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
show,XStringPartialMatches-method |
XStringPartialMatches objects |
show,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
show,XStringViews-method |
The XStringViews class |
start,IRanges-method |
IRanges and NormalIRanges objects |
start<-,UnlockedIRanges-method |
IRanges and NormalIRanges objects |
startIndex |
Searching a sequence for patterns stored in a dictionary |
startIndex,ByName_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
startIndex,ByPos_MIndex-method |
Searching a sequence for patterns stored in a dictionary |
startIndex,MIndex-method |
Searching a sequence for patterns stored in a dictionary |
strrev |
Functions to calculate the frequency of letters in a biological sequence |
subBString |
Fast substring extraction |
subject |
The XStringViews class |
subject,XStringViews-method |
The XStringViews class |
subpatterns |
XStringPartialMatches objects |
subpatterns,XStringPartialMatches-method |
XStringPartialMatches objects |
subseq |
BString objects |
subseq,MaskedXString-method |
MaskedXString objects |
subseq,XString-method |
BString objects |
substitution.matrices |
Scoring matrices |
substr |
Fast substring extraction |
substr,XString-method |
Fast substring extraction |
substring |
Fast substring extraction |
substring,XString-method |
Fast substring extraction |
subviews |
Basic functions for creating or modifying XStringViews objects |
subXString |
Fast substring extraction |
XString |
BString objects |
XString,AsIs-method |
BString objects |
XString,character-method |
BString objects |
XString,MaskedXString-method |
MaskedXString objects |
XString,XString-method |
BString objects |
XString-class |
BString objects |
XStringAlign |
XStringAlign objects |
XStringAlign-class |
XStringAlign objects |
XStringList |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringList-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringPartialMatches-class |
XStringPartialMatches objects |
XStringSet |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet,AsIs-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet,character-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet,XString-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet,XStringSet-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet,XStringViews-method |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSet-class |
BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects |
XStringSetToFASTArecords |
Read/write an XStringSet or XStringViews object from/to a file |
XStringViews |
Basic functions for creating or modifying XStringViews objects |
XStringViews,ANY-method |
Basic functions for creating or modifying XStringViews objects |
XStringViews,file-method |
Basic functions for creating or modifying XStringViews objects |
XStringViews,XString-method |
Basic functions for creating or modifying XStringViews objects |
XStringViews,XStringViews-method |
Basic functions for creating or modifying XStringViews objects |
XStringViews-class |
The XStringViews class |
XStringViews-constructors |
Basic functions for creating or modifying XStringViews objects |