TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis
Version 1.14.0

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]
Bioconductor views Alignment GeneRegulation MotifAnnotation MotifDiscovery Transcription
Date of publicationNone
MaintainerGe Tan <ge.tan09@imperial.ac.uk>
LicenseGPL-2
Version1.14.0
URL https://github.com/ge11232002/TFBSTools
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TFBSTools")

Getting started

Package overview
Transcription factor binding site (TFBS) analysis with the \"TFBSTools\" package

Popular man pages

getMatrixSet-methods: Advanced JASPAR database search functions 'get_MatrixSet'
parseMEMEOutput: parseMEMEOutput
runMEME-methods: Wrapper function for MEME
searchSeq-methods: searchSeq method
seqLogo: Plot a sequence logo
SiteSet-class: Class '"SiteSet"'
XMatrixList-class: Class '"XMatrixList"'
See all...

All man pages Function index File listing

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"'
parseMEMEOutput: parseMEMEOutput
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

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
TAXIDToSpecies Source code
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
create_tables Source code
deleteMatrixHavingID Man page
deleteMatrixHavingID,JASPAR2014-method Man page
deleteMatrixHavingID,JASPAR2016-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
fillDBOptsWithDefaults Source code
findLargestOverlaps Source code
fixTAXID 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,SQLiteConnection-method Man page
getMatrixByID,character-method Man page
getMatrixByName Man page
getMatrixByName,JASPAR2014-method Man page
getMatrixByName,JASPAR2016-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,SQLiteConnection-method Man page
getMatrixSet,character-method Man page
getPosProb Man page
getPosProb,TFFMDetail-method Man page
getPosProb,TFFMFirst-method Man page
get_IDlist_by_query Source code
get_Matrix_by_int_id Source code
get_internal_id Source code
get_latest_version Source code
initializeJASPARDB Man page
initializeJASPARDB,JASPAR2014-method Man page
initializeJASPARDB,JASPAR2016-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
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
processJASPARText Source code
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
s_latest_version 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
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,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
store_matrix Source code
store_matrix_acc Source code
store_matrix_annotation Source code
store_matrix_data Source code
store_matrix_species Source code
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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.r
R/AllGenerics.r
R/DB-methods.r
R/DirichletMixture.r
R/Enrichment.R
R/ICM-methods.r
R/IO.R
R/JASPAR.R
R/Motif-methods.r
R/PFM-methods.r
R/PWM-methods.r
R/PairwiseAlignment-methods.r
R/SiteSet-methods.r
R/TFFM.R
R/TFFMseqLogo.R
R/Wrappers-methods.r
R/XMatrix-methods.r
R/XMatrixList-methods.r
R/coercion-methods.r
R/show-methods.r
R/util-methods.r
build
build/vignette.rds
data
data/MA0003.2.rda
data/MA0004.1.rda
data/MA0043.rda
data/MA0048.rda
inst
inst/CITATION
inst/TFBSToolsBuild
inst/TFBSToolsBuild/build.r
inst/TFBSToolsBuild/build2.R
inst/TFBSToolsBuild/timing.R
inst/doc
inst/doc/TFBSTools.R
inst/doc/TFBSTools.Rmd
inst/doc/TFBSTools.html
inst/extdata
inst/extdata/MA0001.1.pfm
inst/extdata/crp0.s
inst/extdata/hg19.danRer7.net.axt
inst/extdata/meme.output
inst/extdata/pfm_all_example.txt
inst/extdata/tffm_detailed.xml
inst/extdata/tffm_first_order.xml
inst/obsolete
inst/obsolete/PairwiseAlignmentTFBS-class.Rd
inst/obsolete/TFBSTools.Rnw
inst/obsolete/matrixAligner.c
man
man/IUPAC2Matrix.Rd
man/MA0004.1.Rd
man/MotifSet-class.Rd
man/PFMSimilarity-methods.Rd
man/PWMSimilarity-methods.Rd
man/SitePairSet-class.Rd
man/SitePairSetList-class.Rd
man/SiteSet-class.Rd
man/SiteSetList-class.Rd
man/TFBSTools-package.Rd
man/TFFM-class.Rd
man/XMatrix-class.Rd
man/XMatrixList-class.Rd
man/calConservation-methods.Rd
man/deleteMatrixHavingID-methods.Rd
man/dmmEM-methods.Rd
man/getEmissionProb.Rd
man/getMatrixByID-methods.Rd
man/getMatrixSet-methods.Rd
man/getPosProb.Rd
man/makeFlatFileDir.Rd
man/parseMEMEOutput.Rd
man/permuteMatrix-methods.Rd
man/rPWMDmm-methods.Rd
man/readJASPARMatrix.Rd
man/readXMLTFFM.Rd
man/runMEME-methods.Rd
man/sampleRanges.Rd
man/searchAln-methods.Rd
man/searchPairBSgenome-methods.Rd
man/searchSeq-methods.Rd
man/seqLogo.Rd
man/shannon.entropy.Rd
man/toGRangesList-methods.Rd
man/toICM-methods.Rd
man/toPWM-methods.Rd
man/writeGFF3-methods.Rd
src
src/Makevars
src/Makevars.common
src/Makevars.win
src/R_init_TFBSTools.c
src/TFBSTools.h
src/matrixAlignerDynamic.c
tests
tests/testthat
tests/testthat.R
tests/testthat/test_MEME.R
tests/testthat/test_PFM.R
tests/testthat/test_TFFM.R
tests/testthat/test_XMatrix-class.R
tests/testthat/test_searchSeq.R
vignettes
vignettes/TFBSTools.Rmd
vignettes/TFBSTools.bib
TFBSTools documentation built on May 20, 2017, 10:06 p.m.

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