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

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

AuthorGe Tan [aut, cre]
Date of publicationNone
MaintainerGe Tan <ge.tan09@imperial.ac.uk>
LicenseGPL-2
Version1.12.1
https://github.com/ge11232002/TFBSTools

View on Bioconductor

Man pages

calConservation-methods: calConservation method

deleteMatrixHavingID-methods: JASPAR database operations

dmmEM-methods: dmmEM method

getEmissionProb: Get the emission distribution parameters.

getMatrixByID-methods: Basic JASPAR database search functionis 'getMatrixByID',...

getMatrixSet-methods: Advanced JASPAR database search functions 'get_MatrixSet'

getPosProb: Get the emission probabilities of nucleotides

IUPAC2Matrix: IUPAC2Matrix

MA0004.1: Some example PFM matrices.

makeFlatFileDir: Generate "FlatFileDir" directory

MotifSet-class: Class '"MotifSet"'

permuteMatrix-methods: permuteMatrix method

PFMSimilarity-methods: PFMSimilarity method

PWMSimilarity-methods: PWMSimilarity method

readJASPARMatrix: Read JASPAR format matrix

readXMLTFFM: readXMLTFFM

rPWMDmm-methods: rPWMDmm method

runMEME-methods: Wrapper function for MEME

sampleRanges: sampleRanges

searchAln-methods: searchAln method

searchPairBSgenome-methods: searchPairBSgenome method

searchSeq-methods: searchSeq method

seqLogo: Plot a sequence logo

shannon.entropy: Calculate the Shannon entropy

SitePairSet-class: Class '"SitePairSet"'

SitePairSetList-class: Class '"SitePairSetList"'

SiteSet-class: Class '"SiteSet"'

SiteSetList-class: Class '"SiteSetList"'

TFBSTools-package: TFBS software package.

TFFM-class: The TFFM class

toGRangesList-methods: toGRangesList function

toICM-methods: toICM method

toPWM-methods: toPWM method

writeGFF3-methods: 'writeGFF3', 'writeGFF2' functions

XMatrix-class: '"XMatrix"' objects

XMatrixList-class: Class '"XMatrixList"'

Functions

as.data.frame,SitePairSetList-method Man page
as.data.frame,SitePairSet-method Man page
as.data.frame,SiteSetList-method Man page
as.data.frame,SiteSet-method Man page
as.matrix,XMatrix-method Man page
bg Man page
bg,XMatrixList-method Man page
bg<-,XMatrix-method Man page
bg,XMatrix-method Man page
calConservation Man page
calConservation,character,character-method Man page
calConservation,character,missing-method Man page
calConservation,DNAString,DNAString-method Man page
calConservation,DNAStringSet,missing-method Man page
calConservation-methods Man page
c-methods Man page
colSums,XMatrix-method Man page
consensusMatrix,MotifSet-method Man page
c,SiteSet-method Man page
deleteMatrixHavingID Man page
deleteMatrixHavingID,character-method Man page
deleteMatrixHavingID,JASPAR2014-method Man page
deleteMatrixHavingID,JASPAR2016-method Man page
deleteMatrixHavingID,SQLiteConnection-method Man page
dim,XMatrix-method Man page
dmmEM Man page
dmmEM,ANY-method Man page
dmmEM,matrix-method Man page
dmmEM-methods Man page
dmmEM,PFMatrixList-method Man page
end,SiteSet-method Man page
getEmissionProb Man page
getEmissionProb,TFFMDetail-method Man page
getEmissionProb,TFFMFirst-method Man page
getMatrixByID Man page
getMatrixByID,character-method Man page
getMatrixByID,JASPAR2014-method Man page
getMatrixByID,JASPAR2016-method Man page
getMatrixByID,SQLiteConnection-method Man page
getMatrixByName Man page
getMatrixByName,character-method Man page
getMatrixByName,JASPAR2014-method Man page
getMatrixByName,JASPAR2016-method Man page
getMatrixByName,SQLiteConnection-method Man page
getMatrixSet Man page
getMatrixSet,character-method Man page
getMatrixSet,JASPAR2014-method Man page
getMatrixSet,JASPAR2016-method Man page
getMatrixSet,SQLiteConnection-method Man page
getPosProb Man page
getPosProb,TFFMDetail-method Man page
getPosProb,TFFMFirst-method Man page
ICMatrix Man page
ICMatrix-class Man page
ICMatrixList Man page
ICMatrixList-class Man page
ID Man page
ID,XMatrixList-method Man page
ID<-,XMatrix-method Man page
ID,XMatrix-method Man page
initializeJASPARDB Man page
initializeJASPARDB,character-method Man page
initializeJASPARDB,JASPAR2014-method Man page
initializeJASPARDB,JASPAR2016-method Man page
initializeJASPARDB,SQLiteConnection-method Man page
IUPAC2Matrix Man page
length-methods Man page
length,MotifSet-method Man page
length,SitePairSet-method Man page
length,SiteSet-method Man page
length,XMatrix-method Man page
MA0003.2 Man page
MA0004.1 Man page
MA0043 Man page
MA0048 Man page
makeFlatFileDir Man page
Matrix Man page
Matrix<- Man page
matrixClass Man page
matrixClass,XMatrixList-method Man page
matrixClass<-,XMatrix-method Man page
matrixClass,XMatrix-method Man page
matrixType Man page
matrixType,ICMatrix-method Man page
matrixType-methods Man page
matrixType,PFMatrix-method Man page
matrixType,PWMatrix-method Man page
matrixType,XMatrixList-method Man page
Matrix,XMatrixList-method Man page
Matrix<-,XMatrix-method Man page
Matrix,XMatrix-method Man page
[-methods Man page
MotifSet Man page
[,MotifSet,ANY,ANY,ANY-method Man page
[,MotifSet,ANY,ANY-method Man page
MotifSet-class Man page
[,MotifSet-method Man page
name Man page
name,XMatrixList-method Man page
name<-,XMatrix-method Man page
name,XMatrix-method Man page
ncol,TFFMDetail-method Man page
ncol,TFFMFirst-method Man page
ncol,XMatrix-method Man page
pattern,SiteSet-method Man page
permuteMatrix Man page
permuteMatrix,matrix-method Man page
permuteMatrix-methods Man page
permuteMatrix,PFMatrixList-method Man page
permuteMatrix,PFMatrix-method Man page
PFMatrix Man page
PFMatrix-class Man page
PFMatrixList Man page
PFMatrixList-class Man page
PFMSimilarity Man page
PFMSimilarity,matrix,character-method Man page
PFMSimilarity,matrix,matrix-method Man page
PFMSimilarity,matrix,PFMatrix-method Man page
PFMSimilarity-methods Man page
PFMSimilarity,PFMatrix,character-method Man page
PFMSimilarity,PFMatrixList,character-method Man page
PFMSimilarity,PFMatrixList,matrix-method Man page
PFMSimilarity,PFMatrixList,PFMatrix-method Man page
PFMSimilarity,PFMatrix,matrix-method Man page
PFMSimilarity,PFMatrix,PFMatrix-method Man page
primary,SiteSet-method Man page
pvalues Man page
pvalues,SiteSetList-method Man page
pvalues,SiteSet-method Man page
PWMatrix Man page
PWMatrix-class Man page
PWMatrixList Man page
PWMatrixList-class Man page
PWMSimilarity Man page
PWMSimilarity,matrix,matrix-method Man page
PWMSimilarity,matrix,PWMatrix-method Man page
PWMSimilarity-methods Man page
PWMSimilarity,PWMatrixList,matrix-method Man page
PWMSimilarity,PWMatrixList,PWMatrixList-method Man page
PWMSimilarity,PWMatrixList,PWMatrix-method Man page
PWMSimilarity,PWMatrix,matrix-method Man page
PWMSimilarity,PWMatrix,PWMatrix-method Man page
readJASPARMatrix Man page
readXMLTFFM Man page
relScore Man page
relScore,SiteSetList-method Man page
relScore,SiteSet-method Man page
reverseComplement,XMatrix-method Man page
rowSums,XMatrix-method Man page
rPWMDmm Man page
rPWMDmm,matrix-method Man page
rPWMDmm-methods Man page
rPWMDmm,PFMatrixList-method Man page
rPWMDmm,PFMatrix-method Man page
runMEME Man page
runMEME,character-method Man page
runMEME,DNAStringSet-method Man page
sampleRanges Man page
score,SiteSet-method Man page
searchAln Man page
searchAln,PWMatrix,Axt,missing-method Man page
searchAln,PWMatrix,character,character-method Man page
searchAln,PWMatrix,character,missing-method Man page
searchAln,PWMatrix,DNAString,DNAString-method Man page
searchAln,PWMatrix,DNAStringSet,missing-method Man page
searchAln,PWMatrixList,character,character-method Man page
searchAln,PWMatrixList,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,PWMatrix,PairwiseAlignmentTFBS,missing-method Man page
searchPairBSgenome Man page
searchPairBSgenome-methods Man page
searchPairBSgenome,PWMatrixList-method Man page
searchPairBSgenome,PWMatrix-method Man page
searchSeq Man page
searchSeq-methods Man page
searchSeq,PWMatrixList-method Man page
searchSeq,PWMatrix-method Man page
seqLogo Man page
seqLogo,ICMatrix-method Man page
seqLogo,TFFM-method Man page
seqname,SiteSet-method Man page
shannon.entropy Man page
show,SiteSet-method Man page
site1,SitePairSet-method Man page
site2,SitePairSet-method Man page
SitePairSet Man page
SitePairSet-class Man page
SitePairSetList Man page
SitePairSetList-class Man page
SiteSet Man page
[,SiteSet,ANY,ANY,ANY-method Man page
[,SiteSet,ANY,ANY-method Man page
SiteSet-class Man page
SiteSetList Man page
SiteSetList-class Man page
[,SiteSet-method Man page
sitesource,SiteSet-method Man page
sitesSeq Man page
sitesSeq,MotifSet-method Man page
start,SiteSet-method Man page
storeMatrix Man page
storeMatrix,character,PFMatrixList-method Man page
storeMatrix,character,PFMatrix-method Man page
storeMatrix,JASPAR2014,PFMatrixList-method Man page
storeMatrix,JASPAR2014,PFMatrix-method Man page
storeMatrix,JASPAR2016,PFMatrixList-method Man page
storeMatrix,JASPAR2016,PFMatrix-method Man page
storeMatrix-methods Man page
storeMatrix,SQLiteConnection,PFMatrixList-method Man page
storeMatrix,SQLiteConnection,PFMatrix-method Man page
strand,SiteSet-method Man page
strand,XMatrixList-method Man page
strand<-,XMatrix-method Man page
strand,XMatrix-method Man page
tags Man page
tags,XMatrixList-method Man page
tags,XMatrix-method Man page
TFBSTools Man page
TFFM Man page
TFFMDetail Man page
TFFMFirst Man page
toGRangesList Man page
toGRangesList-methods Man page
toGRangesList,SitePairSetList,Axt-method Man page
toICM Man page
toICM,character-method Man page
toICM,DNAStringSet-method Man page
toICM,matrix-method Man page
toICM,PFMatrixList-method Man page
toICM,PFMatrix-method Man page
toPWM Man page
toPWM,character-method Man page
toPWM,DNAStringSet-method Man page
toPWM,matrix-method Man page
toPWM,PFMatrixList-method Man page
toPWM,PFMatrix-method Man page
totalIC Man page
totalIC,ICMatrix-method Man page
totalIC-methods Man page
totalIC,TFFM-method Man page
views Man page
views,SiteSet-method Man page
writeGFF2 Man page
writeGFF2-methods Man page
writeGFF2,SitePairSetList-method Man page
writeGFF2,SitePairSet-method Man page
writeGFF2,SiteSetList-method Man page
writeGFF2,SiteSet-method Man page
writeGFF3 Man page
writeGFF3-methods Man page
writeGFF3,SitePairSetList-method Man page
writeGFF3,SitePairSet-method Man page
writeGFF3,SiteSetList-method Man page
writeGFF3,SiteSet-method Man page
XMatrix Man page
XMatrix-class Man page
XMatrixList Man page
XMatrixList,list-method Man page

Files

TFBSTools/DESCRIPTION
TFBSTools/NAMESPACE
TFBSTools/NEWS
TFBSTools/R
TFBSTools/R/AllClasses.r
TFBSTools/R/AllGenerics.r
TFBSTools/R/DB-methods.r
TFBSTools/R/DirichletMixture.r
TFBSTools/R/Enrichment.R
TFBSTools/R/ICM-methods.r
TFBSTools/R/IO.R TFBSTools/R/JASPAR.R
TFBSTools/R/Motif-methods.r
TFBSTools/R/PFM-methods.r
TFBSTools/R/PWM-methods.r
TFBSTools/R/PairwiseAlignment-methods.r
TFBSTools/R/SiteSet-methods.r
TFBSTools/R/TFFM.R TFBSTools/R/TFFMseqLogo.R
TFBSTools/R/Wrappers-methods.r
TFBSTools/R/XMatrix-methods.r
TFBSTools/R/XMatrixList-methods.r
TFBSTools/R/coercion-methods.r
TFBSTools/R/show-methods.r
TFBSTools/R/util-methods.r
TFBSTools/build
TFBSTools/build/vignette.rds
TFBSTools/data
TFBSTools/data/MA0003.2.rda
TFBSTools/data/MA0004.1.rda
TFBSTools/data/MA0043.rda
TFBSTools/data/MA0048.rda
TFBSTools/inst
TFBSTools/inst/CITATION
TFBSTools/inst/TFBSToolsBuild
TFBSTools/inst/TFBSToolsBuild/build.r
TFBSTools/inst/TFBSToolsBuild/build2.R
TFBSTools/inst/TFBSToolsBuild/timing.R
TFBSTools/inst/doc
TFBSTools/inst/doc/TFBSTools.R
TFBSTools/inst/doc/TFBSTools.Rmd
TFBSTools/inst/doc/TFBSTools.html
TFBSTools/inst/extdata
TFBSTools/inst/extdata/MA0001.1.pfm
TFBSTools/inst/extdata/crp0.s
TFBSTools/inst/extdata/hg19.danRer7.net.axt
TFBSTools/inst/extdata/pfm_all_example.txt
TFBSTools/inst/extdata/tffm_detailed.xml
TFBSTools/inst/extdata/tffm_first_order.xml
TFBSTools/inst/obsolete
TFBSTools/inst/obsolete/PairwiseAlignmentTFBS-class.Rd
TFBSTools/inst/obsolete/TFBSTools.Rnw
TFBSTools/inst/obsolete/matrixAligner.c
TFBSTools/man
TFBSTools/man/IUPAC2Matrix.Rd TFBSTools/man/MA0004.1.Rd TFBSTools/man/MotifSet-class.Rd TFBSTools/man/PFMSimilarity-methods.Rd TFBSTools/man/PWMSimilarity-methods.Rd TFBSTools/man/SitePairSet-class.Rd TFBSTools/man/SitePairSetList-class.Rd TFBSTools/man/SiteSet-class.Rd TFBSTools/man/SiteSetList-class.Rd TFBSTools/man/TFBSTools-package.Rd TFBSTools/man/TFFM-class.Rd TFBSTools/man/XMatrix-class.Rd TFBSTools/man/XMatrixList-class.Rd TFBSTools/man/calConservation-methods.Rd TFBSTools/man/deleteMatrixHavingID-methods.Rd TFBSTools/man/dmmEM-methods.Rd TFBSTools/man/getEmissionProb.Rd TFBSTools/man/getMatrixByID-methods.Rd TFBSTools/man/getMatrixSet-methods.Rd TFBSTools/man/getPosProb.Rd TFBSTools/man/makeFlatFileDir.Rd TFBSTools/man/permuteMatrix-methods.Rd TFBSTools/man/rPWMDmm-methods.Rd TFBSTools/man/readJASPARMatrix.Rd TFBSTools/man/readXMLTFFM.Rd TFBSTools/man/runMEME-methods.Rd TFBSTools/man/sampleRanges.Rd TFBSTools/man/searchAln-methods.Rd TFBSTools/man/searchPairBSgenome-methods.Rd TFBSTools/man/searchSeq-methods.Rd TFBSTools/man/seqLogo.Rd TFBSTools/man/shannon.entropy.Rd TFBSTools/man/toGRangesList-methods.Rd TFBSTools/man/toICM-methods.Rd TFBSTools/man/toPWM-methods.Rd TFBSTools/man/writeGFF3-methods.Rd
TFBSTools/src
TFBSTools/src/Makevars
TFBSTools/src/Makevars.common
TFBSTools/src/Makevars.win
TFBSTools/src/R_init_TFBSTools.c
TFBSTools/src/TFBSTools.h
TFBSTools/src/matrixAlignerDynamic.c
TFBSTools/tests
TFBSTools/tests/testthat
TFBSTools/tests/testthat.R
TFBSTools/tests/testthat/test_PFM.R
TFBSTools/tests/testthat/test_TFFM.R
TFBSTools/tests/testthat/test_XMatrix-class.R
TFBSTools/tests/testthat/test_searchSeq.R
TFBSTools/vignettes
TFBSTools/vignettes/TFBSTools.Rmd
TFBSTools/vignettes/TFBSTools.bib

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