| 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 |