Software Package for Transcription Factor Binding Site (TFBS) Analysis


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Documentation for package ‘TFBSTools’ version 1.40.0

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A B C D E G I L M N P R S T V W X misc

-- A --

as.data.frame-method Class '"SitePairSet"'
as.data.frame-method Class '"SitePairSetList"'
as.data.frame-method Class '"SiteSet"'
as.data.frame-method Class '"SiteSetList"'
as.matrix-method '"XMatrix"' objects

-- B --

bg '"XMatrix"' objects
bg-method '"XMatrix"' objects
bg-method Class '"XMatrixList"'
bg<--method '"XMatrix"' objects

-- C --

c-method Class '"SiteSet"'
c-methods Class '"SiteSet"'
calConservation calConservation method
calConservation-method calConservation method
calConservation-methods calConservation method
colSums-method '"XMatrix"' objects
consensusMatrix-method Class '"MotifSet"'

-- D --

deleteMatrixHavingID JASPAR database operations
deleteMatrixHavingID-method JASPAR database operations
dim-method '"XMatrix"' objects
dmmEM dmmEM method
dmmEM-method dmmEM method
dmmEM-methods dmmEM method

-- E --

end-method Class '"SiteSet"'

-- G --

getEmissionProb Get the emission distribution parameters.
getEmissionProb-method Get the emission distribution parameters.
getMatrixByID Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByID-method Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByName Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByName-method Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixSet Advanced JASPAR database search functions 'get_MatrixSet'
getMatrixSet-method Advanced JASPAR database search functions 'get_MatrixSet'
getPosProb Get the emission probabilities of nucleotides
getPosProb-method Get the emission probabilities of nucleotides

-- I --

ICMatrix '"XMatrix"' objects
ICMatrix-class '"XMatrix"' objects
ICMatrixList Class '"XMatrixList"'
ICMatrixList-class Class '"XMatrixList"'
ID '"XMatrix"' objects
ID-method '"XMatrix"' objects
ID-method Class '"XMatrixList"'
ID<--method '"XMatrix"' objects
initializeJASPARDB JASPAR database operations
initializeJASPARDB-method JASPAR database operations
IUPAC2Matrix IUPAC2Matrix

-- L --

length-method Class '"MotifSet"'
length-method Class '"SitePairSet"'
length-method Class '"SiteSet"'
length-method '"XMatrix"' objects
length-methods '"XMatrix"' objects

-- M --

MA0003.2 Some example PFM matrices.
MA0004.1 Some example PFM matrices.
MA0043 Some example PFM matrices.
MA0048 Some example PFM matrices.
makeFlatFileDir Generate "FlatFileDir" directory
Matrix '"XMatrix"' objects
Matrix-method '"XMatrix"' objects
Matrix-method Class '"XMatrixList"'
Matrix<- '"XMatrix"' objects
Matrix<--method '"XMatrix"' objects
matrixClass '"XMatrix"' objects
matrixClass-method '"XMatrix"' objects
matrixClass-method Class '"XMatrixList"'
matrixClass<--method '"XMatrix"' objects
matrixType '"XMatrix"' objects
matrixType-method '"XMatrix"' objects
matrixType-method Class '"XMatrixList"'
matrixType-methods '"XMatrix"' objects
MotifSet Class '"MotifSet"'
MotifSet-class Class '"MotifSet"'

-- N --

name '"XMatrix"' objects
name-method '"XMatrix"' objects
name-method Class '"XMatrixList"'
name<--method '"XMatrix"' objects
ncol-method The TFFM class
ncol-method '"XMatrix"' objects

-- P --

parseMEMEOutput parseMEMEOutput
pattern-method Class '"SiteSet"'
permuteMatrix permuteMatrix method
permuteMatrix-method permuteMatrix method
permuteMatrix-methods permuteMatrix method
PFMatrix '"XMatrix"' objects
PFMatrix-class '"XMatrix"' objects
PFMatrixList Class '"XMatrixList"'
PFMatrixList-class Class '"XMatrixList"'
PFMSimilarity PFMSimilarity method
PFMSimilarity-method PFMSimilarity method
PFMSimilarity-methods PFMSimilarity method
primary-method Class '"SiteSet"'
pvalues Class '"SiteSet"'
pvalues-method Class '"SiteSet"'
pvalues-method Class '"SiteSetList"'
PWMatrix '"XMatrix"' objects
PWMatrix-class '"XMatrix"' objects
PWMatrixList Class '"XMatrixList"'
PWMatrixList-class Class '"XMatrixList"'
PWMSimilarity PWMSimilarity method
PWMSimilarity-method PWMSimilarity method
PWMSimilarity-methods PWMSimilarity method

-- R --

readJASPARMatrix Read JASPAR format matrix
readXMLTFFM readXMLTFFM
relScore Class '"SiteSet"'
relScore-method Class '"SiteSet"'
relScore-method Class '"SiteSetList"'
reverseComplement-method '"XMatrix"' objects
rowSums-method '"XMatrix"' objects
rPWMDmm rPWMDmm method
rPWMDmm-method rPWMDmm method
rPWMDmm-methods rPWMDmm method
runMEME Wrapper function for MEME
runMEME-method Wrapper function for MEME

-- S --

sampleRanges sampleRanges
score-method Class '"SiteSet"'
searchAln searchAln method
searchAln-method searchAln method
searchPairBSgenome searchPairBSgenome method
searchPairBSgenome-method searchPairBSgenome method
searchPairBSgenome-methods searchPairBSgenome method
searchSeq searchSeq method
searchSeq-method searchSeq method
searchSeq-methods searchSeq method
seqLogo Plot a sequence logo
seqLogo-method Plot a sequence logo
seqname-method Class '"SiteSet"'
shannon.entropy Calculate the Shannon entropy
show-method Class '"SiteSet"'
showAsCell-method Class '"XMatrixList"'
site1-method Class '"SitePairSet"'
site2-method Class '"SitePairSet"'
SitePairSet Class '"SitePairSet"'
SitePairSet-class Class '"SitePairSet"'
SitePairSetList Class '"SitePairSetList"'
SitePairSetList-class Class '"SitePairSetList"'
SiteSet Class '"SiteSet"'
SiteSet-class Class '"SiteSet"'
SiteSetList Class '"SiteSetList"'
SiteSetList-class Class '"SiteSetList"'
sitesource-method Class '"SiteSet"'
sitesSeq Class '"MotifSet"'
sitesSeq-method Class '"MotifSet"'
start-method Class '"SiteSet"'
storeMatrix JASPAR database operations
storeMatrix-method JASPAR database operations
storeMatrix-methods JASPAR database operations
strand-method Class '"SiteSet"'
strand-method '"XMatrix"' objects
strand-method Class '"XMatrixList"'
strand<--method '"XMatrix"' objects

-- T --

tags '"XMatrix"' objects
tags-method '"XMatrix"' objects
tags-method Class '"XMatrixList"'
TFBSTools TFBS software package.
TFFM The TFFM class
TFFMDetail The TFFM class
TFFMFirst The TFFM class
toGRangesList toGRangesList function
toGRangesList-method toGRangesList function
toGRangesList-methods toGRangesList function
toICM toICM method
toICM-method toICM method
toPWM toPWM method
toPWM-method toPWM method
totalIC '"XMatrix"' objects
totalIC-method The TFFM class
totalIC-method '"XMatrix"' objects
totalIC-methods '"XMatrix"' objects

-- V --

views Class '"SiteSet"'
views-method Class '"SiteSet"'

-- W --

writeGFF2 'writeGFF3', 'writeGFF2' functions
writeGFF2-method 'writeGFF3', 'writeGFF2' functions
writeGFF2-methods 'writeGFF3', 'writeGFF2' functions
writeGFF3 'writeGFF3', 'writeGFF2' functions
writeGFF3-method 'writeGFF3', 'writeGFF2' functions
writeGFF3-methods 'writeGFF3', 'writeGFF2' functions

-- X --

XMatrix '"XMatrix"' objects
XMatrix-class '"XMatrix"' objects
XMatrixList Class '"XMatrixList"'
XMatrixList-method Class '"XMatrixList"'

-- misc --

[-method Class '"MotifSet"'
[-method Class '"SiteSet"'
[-methods '"XMatrix"' objects