AAKeySortedData |
Data Dictionaries with XString-based Keys |
AAKeySortedData-class |
Data Dictionaries with XString-based Keys |
AAKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
AAKeySortedDataList-class |
List of Data Dictionaries with XString-based Keys |
AAMultipleAlignment |
MultipleAlignment objects |
AAMultipleAlignment-class |
MultipleAlignment objects |
AAString |
AAString objects |
AAString-class |
AAString objects |
AAStringSet |
XStringSet objects |
AAStringSet-class |
XStringSet objects |
AAStringSetList |
XStringSetList objects |
AAStringSetList-class |
XStringSetList objects |
AA_ALPHABET |
AAString objects |
AA_WCP |
Weighted Clustered Positions (WCP) objects |
AA_WCP-class |
Weighted Clustered Positions (WCP) objects |
ACtree2 |
PDict objects |
ACtree2-class |
PDict objects |
adjacentViews |
Basic functions for creating or modifying XStringViews objects |
align-utils |
Utility functions related to sequence alignment |
aligned |
AlignedXStringSet and QualityAlignedXStringSet objects |
aligned-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
aligned-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet0 |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet0-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
alphabet |
BString objects |
alphabet-method |
BString objects |
alphabetFrequency |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
alphabetFrequency-method |
MultipleAlignment objects |
alphabetFrequency-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
AMINO_ACID_CODE |
The Single-Letter Amino Acid Code |
append-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
as.character-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
as.character-method |
MaskedXString objects |
as.character-method |
MultipleAlignment objects |
as.character-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
as.character-method |
BString objects |
as.character-method |
XStringSet objects |
as.character-method |
The XStringViews class |
as.integer-method |
PhredQuality and SolexaQuality objects |
as.list-method |
PDict objects |
as.matrix-method |
MultipleAlignment objects |
as.matrix-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
as.matrix-method |
PhredQuality and SolexaQuality objects |
as.matrix-method |
XStringSet objects |
as.matrix-method |
The XStringViews class |
as.numeric-method |
PhredQuality and SolexaQuality objects |
cDNA |
DNA/RNA transcription and translation |
CharacterToFASTArecords |
Read/write an XStringSet object from/to a file |
chartr-method |
Translating letters of a sequence |
class:AAKeySortedData |
Data Dictionaries with XString-based Keys |
class:AAKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
class:AAMultipleAlignment |
MultipleAlignment objects |
class:AAString |
AAString objects |
class:AAStringSet |
XStringSet objects |
class:AAStringSetList |
XStringSetList objects |
class:AA_WCP |
Weighted Clustered Positions (WCP) objects |
class:ACtree2 |
PDict objects |
class:AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
class:AlignedXStringSet0 |
AlignedXStringSet and QualityAlignedXStringSet objects |
class:BKeySortedData |
Data Dictionaries with XString-based Keys |
class:BKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
class:BOC2_SubjectString |
BOC\_SubjectString and BOC2\_SubjectString objects |
class:BOC_SubjectString |
BOC\_SubjectString and BOC2\_SubjectString objects |
class:BString |
BString objects |
class:BStringSet |
XStringSet objects |
class:BStringSetList |
XStringSetList objects |
class:ByPos_MIndex |
MIndex objects |
class:B_WCP |
Weighted Clustered Positions (WCP) objects |
class:DNAKeySortedData |
Data Dictionaries with XString-based Keys |
class:DNAKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
class:DNAMultipleAlignment |
MultipleAlignment objects |
class:DNAString |
DNAString objects |
class:DNAStringSet |
XStringSet objects |
class:DNAStringSetList |
XStringSetList objects |
class:DNA_WCP |
Weighted Clustered Positions (WCP) objects |
class:Expanded_TB_PDict |
PDict objects |
class:InDel |
InDel objects |
class:MaskedAAString |
MaskedXString objects |
class:MaskedBString |
MaskedXString objects |
class:MaskedDNAString |
MaskedXString objects |
class:MaskedRNAString |
MaskedXString objects |
class:MaskedXString |
MaskedXString objects |
class:MIndex |
MIndex objects |
class:MTB_PDict |
PDict objects |
class:MultipleAlignment |
MultipleAlignment objects |
class:PairwiseAlignedFixedSubject |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
class:PairwiseAlignedFixedSubjectSummary |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
class:PairwiseAlignedXStringSet |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
class:PDict |
PDict objects |
class:PDict3Parts |
PDict objects |
class:PhredQuality |
PhredQuality and SolexaQuality objects |
class:PreprocessedTB |
PDict objects |
class:QualityAlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
class:QualityScaledAAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
class:QualityScaledBStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
class:QualityScaledDNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
class:QualityScaledRNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
class:QualityScaledXStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
class:RNAKeySortedData |
Data Dictionaries with XString-based Keys |
class:RNAKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
class:RNAMultipleAlignment |
MultipleAlignment objects |
class:RNAString |
RNAString objects |
class:RNAStringSet |
XStringSet objects |
class:RNAStringSetList |
XStringSetList objects |
class:RNA_WCP |
Weighted Clustered Positions (WCP) objects |
class:SolexaQuality |
PhredQuality and SolexaQuality objects |
class:TB_PDict |
PDict objects |
class:Twobit |
PDict objects |
class:WCP |
Weighted Clustered Positions (WCP) objects |
class:XKeySortedData |
Data Dictionaries with XString-based Keys |
class:XKeySortedDataList |
List of Data Dictionaries with XString-based Keys |
class:XString |
BString objects |
class:XStringPartialMatches |
XStringPartialMatches objects |
class:XStringQuality |
PhredQuality and SolexaQuality objects |
class:XStringSet |
XStringSet objects |
class:XStringSetList |
XStringSetList objects |
class:XStringViews |
The XStringViews class |
codons |
DNA/RNA transcription and translation |
codons-method |
DNA/RNA transcription and translation |
coerce-method |
MIndex objects |
coerce-method |
MaskedXString objects |
coerce-method |
MultipleAlignment objects |
coerce-method |
BString objects |
coerce-method |
PhredQuality and SolexaQuality objects |
coerce-method |
XStringSet objects |
coerce-method |
The XStringViews class |
collapse-method |
MaskedXString objects |
colmask |
MultipleAlignment objects |
colmask-method |
MultipleAlignment objects |
colmask<- |
MultipleAlignment objects |
colmask<--method |
MultipleAlignment objects |
compareStrings |
Utility functions related to sequence alignment |
compareStrings-method |
Utility functions related to sequence alignment |
complement |
Sequence reversing and complementing |
complement-method |
Sequence reversing and complementing |
complementedPalindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeArmLength-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeLeftArm-method |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
complementedPalindromeRightArm-method |
Searching a sequence for palindromes or complemented palindromes |
complementSeq |
Complementary sequence. |
computeAllFlinks |
PDict objects |
computeAllFlinks-method |
PDict objects |
consensusMatrix |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
consensusMatrix-method |
MultipleAlignment objects |
consensusMatrix-method |
Utility functions related to sequence alignment |
consensusMatrix-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
consensusString |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
consensusString-method |
MultipleAlignment objects |
consensusString-method |
Calculate the frequency of letters in a biological sequence, or the consensus matrix of a set of sequences |
consensusViews |
MultipleAlignment objects |
consensusViews-method |
MultipleAlignment objects |
countbases |
Obtain the ATCG content of a gene |
countIndex |
MIndex objects |
countIndex-method |
MIndex objects |
countPattern |
String searching functions |
countPattern-method |
BOC\_SubjectString and BOC2\_SubjectString objects |
countPattern-method |
String searching functions |
countPDict |
Matching a dictionary of patterns against a reference |
countPDict-method |
Matching a dictionary of patterns against a reference |
countPWM |
PWM creating, matching, and related utilities |
countPWM-method |
PWM creating, matching, and related utilities |
countWCP |
A simple WCP matching function and related utilities |
countWCP-method |
A simple WCP matching function and related utilities |
coverage-method |
Utility functions related to sequence alignment |
coverage-method |
Utility functions operating on the matches returned by a high-level matching function |
mask |
Masking by content (or by position) |
MaskedAAString |
MaskedXString objects |
MaskedAAString-class |
MaskedXString objects |
MaskedBString |
MaskedXString objects |
MaskedBString-class |
MaskedXString objects |
maskeddim |
MultipleAlignment objects |
maskeddim-method |
MultipleAlignment objects |
MaskedDNAString |
MaskedXString objects |
MaskedDNAString-class |
MaskedXString objects |
maskedncol |
MultipleAlignment objects |
maskedncol-method |
MultipleAlignment objects |
maskednrow |
MultipleAlignment objects |
maskednrow-method |
MultipleAlignment objects |
maskedratio-method |
MaskedXString objects |
maskedratio-method |
MultipleAlignment objects |
MaskedRNAString |
MaskedXString objects |
MaskedRNAString-class |
MaskedXString objects |
maskedwidth-method |
MaskedXString objects |
MaskedXString |
MaskedXString objects |
MaskedXString-class |
MaskedXString objects |
maskGaps |
MultipleAlignment objects |
maskGaps-method |
MultipleAlignment objects |
maskMotif |
Masking by content (or by position) |
maskMotif-method |
MultipleAlignment objects |
maskMotif-method |
Masking by content (or by position) |
masks |
MaskedXString objects |
masks-method |
MaskedXString objects |
masks<- |
MaskedXString objects |
masks<--method |
MaskedXString objects |
match-method |
XStringSet objects |
match-utils |
Utility functions operating on the matches returned by a high-level matching function |
matchLRPatterns |
Find paired matches in a sequence |
matchLRPatterns-method |
Find paired matches in a sequence |
matchPattern |
String searching functions |
matchPattern-method |
BOC\_SubjectString and BOC2\_SubjectString objects |
matchPattern-method |
String searching functions |
matchPDict |
Matching a dictionary of patterns against a reference |
matchPDict-exact |
Matching a dictionary of patterns against a reference |
matchPDict-inexact |
Inexact matching with matchPDict()/countPDict()/whichPDict() |
matchPDict-method |
Matching a dictionary of patterns against a reference |
matchProbePair |
Find "theoretical amplicons" mapped to a probe pair |
matchProbePair-method |
Find "theoretical amplicons" mapped to a probe pair |
matchprobes |
A function to match a query sequence to the sequences of a set of probes. |
matchPWM |
PWM creating, matching, and related utilities |
matchPWM-method |
PWM creating, matching, and related utilities |
matchWCP |
A simple WCP matching function and related utilities |
matchWCP-method |
A simple WCP matching function and related utilities |
maxScore |
PWM creating, matching, and related utilities |
maxScore-method |
PWM creating, matching, and related utilities |
maxWeights |
PWM creating, matching, and related utilities |
maxWeights-method |
Weighted Clustered Positions (WCP) objects |
maxWeights-method |
PWM creating, matching, and related utilities |
mergeIUPACLetters |
The IUPAC Extended Genetic Alphabet |
MIndex |
MIndex objects |
MIndex-class |
MIndex objects |
minScore |
PWM creating, matching, and related utilities |
minScore-method |
PWM creating, matching, and related utilities |
minWeights |
PWM creating, matching, and related utilities |
minWeights-method |
PWM creating, matching, and related utilities |
misc |
Some miscellaneous stuff |
mismatch |
Utility functions operating on the matches returned by a high-level matching function |
mismatch-method |
Utility functions related to sequence alignment |
mismatch-method |
Utility functions operating on the matches returned by a high-level matching function |
mismatchSummary |
Utility functions related to sequence alignment |
mismatchSummary-method |
Utility functions related to sequence alignment |
mismatchTable |
Utility functions related to sequence alignment |
mismatchTable-method |
Utility functions related to sequence alignment |
mkAllStrings |
Calculate the frequency of oligonucleotides in a DNA or RNA sequence (and other related functions) |
MTB_PDict |
PDict objects |
MTB_PDict-class |
PDict objects |
MultipleAlignment |
MultipleAlignment objects |
MultipleAlignment-class |
MultipleAlignment objects |
PairwiseAlignedFixedSubject |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubject-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubjectSummary |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedFixedSubjectSummary-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedXStringSet |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedXStringSet-class |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
PairwiseAlignedXStringSet-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
pairwiseAlignment |
Optimal Pairwise Alignment |
pairwiseAlignment-method |
Optimal Pairwise Alignment |
palindromeArmLength |
Searching a sequence for palindromes or complemented palindromes |
palindromeArmLength-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeLeftArm |
Searching a sequence for palindromes or complemented palindromes |
palindromeLeftArm-method |
Searching a sequence for palindromes or complemented palindromes |
palindromeRightArm |
Searching a sequence for palindromes or complemented palindromes |
palindromeRightArm-method |
Searching a sequence for palindromes or complemented palindromes |
PAM120 |
Scoring matrices |
PAM250 |
Scoring matrices |
PAM30 |
Scoring matrices |
PAM40 |
Scoring matrices |
PAM70 |
Scoring matrices |
partitioning |
XStringSetList objects |
partitioning-method |
XStringSetList objects |
pattern |
XStringPartialMatches objects |
pattern-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
pattern-method |
XStringPartialMatches objects |
patternFrequency |
PDict objects |
patternFrequency-method |
PDict objects |
PDict |
PDict objects |
PDict-class |
PDict objects |
PDict-method |
PDict objects |
PDict3Parts |
PDict objects |
PDict3Parts-class |
PDict objects |
phiX174Phage |
Versions of bacteriophage phiX174 complete genome and sample short reads |
PhredQuality |
PhredQuality and SolexaQuality objects |
PhredQuality-class |
PhredQuality and SolexaQuality objects |
pid |
Percent Sequence Identity |
pid-method |
Percent Sequence Identity |
pmatchPattern |
Longest Common Prefix/Suffix/Substring searching functions |
pmatchPattern-method |
Longest Common Prefix/Suffix/Substring searching functions |
PreprocessedTB |
PDict objects |
PreprocessedTB-class |
PDict objects |
print.needwunsQS |
(Deprecated) Needleman-Wunsch Global Alignment |
PWM |
PWM creating, matching, and related utilities |
PWM-method |
PWM creating, matching, and related utilities |
PWMscore |
PWM creating, matching, and related utilities |
PWMscoreStartingAt |
PWM creating, matching, and related utilities |
quality |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
quality-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityAlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
QualityAlignedXStringSet-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
QualityScaledAAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledAAStringSet-class |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledBStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledBStringSet-class |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledDNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledDNAStringSet-class |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledRNAStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledRNAStringSet-class |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledXStringSet |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
QualityScaledXStringSet-class |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
qualitySubstitutionMatrices |
Scoring matrices |
quPhiX174 |
Versions of bacteriophage phiX174 complete genome and sample short reads |
save.XStringSet |
Read/write an XStringSet object from/to a file |
score-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
setdiff-method |
XStringSet objects |
setequal-method |
XStringSet objects |
show-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
show-method |
MIndex objects |
show-method |
MaskedXString objects |
show-method |
MultipleAlignment objects |
show-method |
PDict objects |
show-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
show-method |
QualityScaledBStringSet, QualityScaledDNAStringSet, QualityScaledRNAStringSet and QualityScaledAAStringSet objects |
show-method |
Weighted Clustered Positions (WCP) objects |
show-method |
BString objects |
show-method |
XStringPartialMatches objects |
show-method |
XStringSet objects |
show-method |
XStringSetList objects |
show-method |
The XStringViews class |
SolexaQuality |
PhredQuality and SolexaQuality objects |
SolexaQuality-class |
PhredQuality and SolexaQuality objects |
sort-method |
XStringSet objects |
srPhiX174 |
Versions of bacteriophage phiX174 complete genome and sample short reads |
start-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
startIndex |
MIndex objects |
startIndex-method |
MIndex objects |
stringDist |
String Distance/Alignment Score Matrix |
stringDist-method |
String Distance/Alignment Score Matrix |
strrev |
Sequence reversing and complementing |
subject-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |
subpatterns |
XStringPartialMatches objects |
subpatterns-method |
XStringPartialMatches objects |
subseq-method |
MaskedXString objects |
subseq-method |
XStringSet objects |
subseq<--method |
XStringSet objects |
substitution.matrices |
Scoring matrices |
substr-method |
BString objects |
substring-method |
BString objects |
subXString |
BString objects |
summary-method |
PairwiseAlignedXStringSet, PairwiseAlignedFixedSubject, and PairwiseAlignedFixedSubjectSummary objects |