TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis

Package index
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Vignettes
Functions
348
Source code
33
Man pages
37
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TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis
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API

API for TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis

Global functions
.TAXIDToSpecies Source code
.create_tables Source code
.fillDBOptsWithDefaults Source code
.fixTAXID Source code
.get_IDlist_by_query Source code
.get_Matrix_by_int_id Source code
.get_internal_id Source code
.get_latest_version Source code
.is_latest_version Source code
.processJASPARText Source code
.store_matrix Source code
.store_matrix_acc Source code
.store_matrix_annotation Source code
.store_matrix_data Source code
.store_matrix_species Source code
ICMatrix Man page Source code
ICMatrix-class Man page
ICMatrixList Man page Source code
ICMatrixList-class Man page
ID Man page
ID,XMatrix-method Man page
ID,XMatrixList-method Man page
ID<-,XMatrix-method Man page
IUPAC2Matrix Man page Source code
MA0003.2 Man page
MA0004.1 Man page
MA0043 Man page
MA0048 Man page
MEME Source code
Matrix Man page
Matrix,XMatrix-method Man page
Matrix,XMatrixList-method Man page
Matrix<- Man page
Matrix<-,XMatrix-method Man page
Motif Source code
MotifSet Man page Source code
MotifSet-class Man page
PFMSimilarity Man page
PFMSimilarity,PFMatrix,PFMatrix-method Man page
PFMSimilarity,PFMatrix,character-method Man page
PFMSimilarity,PFMatrix,matrix-method Man page
PFMSimilarity,PFMatrixList,PFMatrix-method Man page
PFMSimilarity,PFMatrixList,character-method Man page
PFMSimilarity,PFMatrixList,matrix-method Man page
PFMSimilarity,matrix,PFMatrix-method Man page
PFMSimilarity,matrix,character-method Man page
PFMSimilarity,matrix,matrix-method Man page
PFMSimilarity-methods Man page
PFMatrix Man page Source code
PFMatrix-class Man page
PFMatrixList Man page Source code
PFMatrixList-class Man page
PWMEuclidean Source code
PWMKL Source code
PWMPearson Source code
PWMSimilarity Man page
PWMSimilarity,PWMatrix,PWMatrix-method Man page
PWMSimilarity,PWMatrix,matrix-method Man page
PWMSimilarity,PWMatrixList,PWMatrix-method Man page
PWMSimilarity,PWMatrixList,PWMatrixList-method Man page
PWMSimilarity,PWMatrixList,matrix-method Man page
PWMSimilarity,matrix,PWMatrix-method Man page
PWMSimilarity,matrix,matrix-method Man page
PWMSimilarity-methods Man page
PWMatrix Man page Source code
PWMatrix-class Man page
PWMatrixList Man page Source code
PWMatrixList-class Man page
PWMrandomizeBayes Source code
PWMscore Source code
SitePairSet Man page Source code
SitePairSet-class Man page
SitePairSetList Man page Source code
SitePairSetList-class Man page
SiteSet Man page Source code
SiteSet-class Man page
SiteSetList Man page Source code
SiteSetList-class Man page
TFBSTools Man page
TFFM Man page
TFFMDetail Man page Source code
TFFMFirst Man page Source code
XMatrix Man page
XMatrix-class Man page
XMatrixList Man page
XMatrixList,list-method Man page
[,MotifSet,ANY,ANY,ANY-method Man page
[,MotifSet,ANY,ANY-method Man page
[,MotifSet-method Man page
[,SiteSet,ANY,ANY,ANY-method Man page
[,SiteSet,ANY,ANY-method Man page
[,SiteSet-method Man page
[-methods Man page
addLetter Source code
as.data.frame,SitePairSet-method Man page
as.data.frame,SitePairSetList-method Man page
as.data.frame,SiteSet-method Man page
as.data.frame,SiteSetList-method Man page
as.matrix,XMatrix-method Man page
bg Man page
bg,XMatrix-method Man page
bg,XMatrixList-method Man page
bg<-,XMatrix-method Man page
c,SiteSet-method Man page
c-methods Man page
calConservation Man page
calConservation,DNAString,DNAString-method Man page
calConservation,DNAStringSet,missing-method Man page
calConservation,character,character-method Man page
calConservation,character,missing-method Man page
calConservation-methods Man page
calculate_conservation Source code
colSums,XMatrix-method Man page
compareMatrix Source code
consensusMatrix,MotifSet-method Man page
deleteMatrixHavingID Man page
deleteMatrixHavingID,JASPAR2014-method Man page
deleteMatrixHavingID,JASPAR2016-method Man page
deleteMatrixHavingID,JASPAR2018-method Man page
deleteMatrixHavingID,JASPAR2020-method Man page
deleteMatrixHavingID,SQLiteConnection-method Man page
deleteMatrixHavingID,character-method Man page
dim,XMatrix-method Man page
dirichletMixtureEMEstimation Source code
dmmEM Man page
dmmEM,ANY-method Man page
dmmEM,PFMatrixList-method Man page
dmmEM,matrix-method Man page
dmmEM-methods Man page
do_PairBSgenomeSearch Source code
do_PairBSgenomeSearchNegative Source code
do_PairBSgenomeSearchNew Source code
do_PairBSgenomeSearchPositive Source code
do_sitesearch Source code
do_sitesearchOneStrand Source code
end,SiteSet-method Man page
findLargestOverlaps Source code
getEmissionProb Man page
getEmissionProb,TFFMDetail-method Man page
getEmissionProb,TFFMFirst-method Man page
getMatrixByID Man page
getMatrixByID,JASPAR2014-method Man page
getMatrixByID,JASPAR2016-method Man page
getMatrixByID,JASPAR2018-method Man page
getMatrixByID,JASPAR2020-method Man page
getMatrixByID,SQLiteConnection-method Man page
getMatrixByID,character-method Man page
getMatrixByName Man page
getMatrixByName,JASPAR2014-method Man page
getMatrixByName,JASPAR2016-method Man page
getMatrixByName,JASPAR2018-method Man page
getMatrixByName,JASPAR2020-method Man page
getMatrixByName,SQLiteConnection-method Man page
getMatrixByName,character-method Man page
getMatrixSet Man page
getMatrixSet,JASPAR2014-method Man page
getMatrixSet,JASPAR2016-method Man page
getMatrixSet,JASPAR2018-method Man page
getMatrixSet,JASPAR2020-method Man page
getMatrixSet,SQLiteConnection-method Man page
getMatrixSet,character-method Man page
getPosProb Man page
getPosProb,TFFMDetail-method Man page
getPosProb,TFFMFirst-method Man page
initializeJASPARDB Man page
initializeJASPARDB,JASPAR2014-method Man page
initializeJASPARDB,JASPAR2016-method Man page
initializeJASPARDB,JASPAR2018-method Man page
initializeJASPARDB,JASPAR2020-method Man page
initializeJASPARDB,SQLiteConnection-method Man page
initializeJASPARDB,character-method Man page
length,MotifSet-method Man page
length,SitePairSet-method Man page
length,SiteSet-method Man page
length,XMatrix-method Man page
length-methods Man page
letterA Source code
letterC Source code
letterG Source code
letterT Source code
makeFlatFileDir Man page Source code
matrixClass Man page
matrixClass,XMatrix-method Man page
matrixClass,XMatrixList-method Man page
matrixClass<-,XMatrix-method Man page
matrixType Man page
matrixType,ICMatrix-method Man page
matrixType,PFMatrix-method Man page
matrixType,PWMatrix-method Man page
matrixType,XMatrixList-method Man page
matrixType-methods Man page
my.searchSeq Source code
name Man page
name,XMatrix-method Man page
name,XMatrixList-method Man page
name<-,XMatrix-method Man page
ncol,TFFMDetail-method Man page
ncol,TFFMFirst-method Man page
ncol,XMatrix-method Man page
normargPfm Source code
normargPriorParams Source code
normargPwm Source code
parseMEMEOutput Man page Source code
parseMEMEOutput412 Source code
pattern,SiteSet-method Man page
permuteMatrix Man page
permuteMatrix,PFMatrix-method Man page
permuteMatrix,PFMatrixList-method Man page
permuteMatrix,matrix-method Man page
permuteMatrix-methods Man page
primary,SiteSet-method Man page
pvalues Man page
pvalues,SiteSet-method Man page
pvalues,SiteSetList-method Man page
rPWMDmm Man page
rPWMDmm,PFMatrix-method Man page
rPWMDmm,PFMatrixList-method Man page
rPWMDmm,matrix-method Man page
rPWMDmm-methods Man page
readJASPARMatrix Man page Source code
readMEME Source code
readXMLTFFM Man page Source code
relScore Man page
relScore,SiteSet-method Man page
relScore,SiteSetList-method Man page
repmat Source code
reverseComplement,XMatrix-method Man page
rowSums,XMatrix-method Man page
runMEME Man page
runMEME,DNAStringSet-method Man page
runMEME,character-method Man page
run_MEME Source code
sampleRanges Man page Source code
sampleRangesOneStrand Source code
schneider_Hnb_approx Source code
schneider_Hnb_exact Source code
schneider_Hnb_precomputed Source code
schneider_correction Source code
score,SiteSet-method Man page
searchAln Man page
searchAln,PWMatrix,Axt,missing-method Man page
searchAln,PWMatrix,DNAString,DNAString-method Man page
searchAln,PWMatrix,DNAStringSet,missing-method Man page
searchAln,PWMatrix,PairwiseAlignmentTFBS,missing-method Man page
searchAln,PWMatrix,character,character-method Man page
searchAln,PWMatrix,character,missing-method Man page
searchAln,PWMatrixList,DNAString,DNAString-method Man page
searchAln,PWMatrixList,DNAStringSet,missing-method Man page
searchAln,PWMatrixList,PairwiseAlignmentTFBS,missing-method Man page
searchAln,PWMatrixList,character,character-method Man page
searchAln,PWMatrixList,character,missing-method Man page
searchPairBSgenome Man page
searchPairBSgenome,PWMatrix-method Man page
searchPairBSgenome,PWMatrixList-method Man page
searchPairBSgenome-methods Man page
searchSeq Man page
searchSeq,PWMatrix-method Man page
searchSeq,PWMatrixList-method Man page
searchSeq-methods Man page
seqLogo Man page
seqLogo,ICMatrix-method Man page
seqLogo,TFFM-method Man page
seqLogoTFFM Source code
seqname,SiteSet-method Man page
shannon.entropy Man page Source code
show,SiteSet-method Man page
showAsCell,XMatrixList-method Man page
site1,SitePairSet-method Man page
site2,SitePairSet-method Man page
sitesSeq Man page
sitesSeq,MotifSet-method Man page
sitesource,SiteSet-method Man page
start,SiteSet-method Man page
storeMatrix Man page
storeMatrix,JASPAR2014,PFMatrix-method Man page
storeMatrix,JASPAR2014,PFMatrixList-method Man page
storeMatrix,JASPAR2016,PFMatrix-method Man page
storeMatrix,JASPAR2016,PFMatrixList-method Man page
storeMatrix,JASPAR2018,PFMatrix-method Man page
storeMatrix,JASPAR2018,PFMatrixList-method Man page
storeMatrix,JASPAR2020,PFMatrix-method Man page
storeMatrix,JASPAR2020,PFMatrixList-method Man page
storeMatrix,SQLiteConnection,PFMatrix-method Man page
storeMatrix,SQLiteConnection,PFMatrixList-method Man page
storeMatrix,character,PFMatrix-method Man page
storeMatrix,character,PFMatrixList-method Man page
storeMatrix-methods Man page
strand,SiteSet-method Man page
strand,XMatrix-method Man page
strand,XMatrixList-method Man page
strand<-,XMatrix-method Man page
tags Man page
tags,XMatrix-method Man page
tags,XMatrixList-method Man page
tfbsEnrichment Source code
toGRangesList Man page
toGRangesList,SitePairSetList,Axt-method Man page
toGRangesList-methods Man page
toICM Man page
toICM,DNAStringSet-method Man page
toICM,PFMatrix-method Man page
toICM,PFMatrixList-method Man page
toICM,character-method Man page
toICM,matrix-method Man page
toPWM Man page
toPWM,DNAStringSet-method Man page
toPWM,PFMatrix-method Man page
toPWM,PFMatrixList-method Man page
toPWM,character-method Man page
toPWM,matrix-method Man page
totalIC Man page
totalIC,ICMatrix-method Man page
totalIC,TFFM-method Man page
totalIC-methods Man page
views Man page
views,SiteSet-method Man page
writeGFF2 Man page
writeGFF2,SitePairSet-method Man page
writeGFF2,SitePairSetList-method Man page
writeGFF2,SiteSet-method Man page
writeGFF2,SiteSetList-method Man page
writeGFF2-methods Man page
writeGFF3 Man page
writeGFF3,SitePairSet-method Man page
writeGFF3,SitePairSetList-method Man page
writeGFF3,SiteSet-method Man page
writeGFF3,SiteSetList-method Man page
writeGFF3-methods Man page
TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.

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