Package: TFBSTools 1.51.0

Ge Tan

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.

Authors:Ge Tan [aut, cre]

TFBSTools_1.51.0.tar.gz
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TFBSTools_1.51.0.tgz(r-4.6-x86_64)TFBSTools_1.51.0.tgz(r-4.6-arm64)TFBSTools_1.51.0.tgz(r-4.5-x86_64)TFBSTools_1.51.0.tgz(r-4.5-arm64)
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TFBSTools_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TFBSTools/json (API)

# Install 'TFBSTools' in R:

install.packages('TFBSTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ge11232002/tfbstools/issues

Datasets:

MA0003.2 - Some example PFM matrices.
MA0004.1 - Some example PFM matrices.
MA0043 - Some example PFM matrices.
MA0048 - Some example PFM matrices.

On BioConductor:TFBSTools-1.51.0(bioc 3.24)TFBSTools-1.50.0(bioc 3.23)

motifannotation generegulation motifdiscovery transcription alignment

11.63 score 35 stars 19 packages 1.8k scripts 33 mentions 67 exports 71 dependencies

Last updated from:f7b3785310. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	264
linux-devel-arm64	NOTE	374
linux-devel-x86_64	NOTE	476
source / vignettes	OK	369
linux-release-arm64	NOTE	383
linux-release-x86_64	NOTE	423
macos-release-arm64	NOTE	330
macos-release-x86_64	NOTE	403
macos-oldrel-arm64	NOTE	338
macos-oldrel-x86_64	NOTE	533
windows-devel	NOTE	435
windows-release	NOTE	395
windows-oldrel	NOTE	390
wasm-release	OK	559

Exports:as.data.frame as.matrix bg calConservation colSums consensusMatrix deleteMatrixHavingID dmmEM end getEmissionProb getMatrixByID getMatrixByName getMatrixSet getPosProb ICMatrix ICMatrixList ID initializeJASPARDB IUPAC2Matrix makeFlatFileDir Matrix Matrix<-matrixClass matrixType MotifSet name ncol parseMEMEOutput permuteMatrix PFMatrix PFMatrixList PFMSimilarity pvalues PWMatrix PWMatrixList PWMSimilarity readJASPARMatrix readXMLTFFM relScore reverseComplement rowSums rPWMDmm runMEME sampleRanges searchAln searchPairBSgenome searchSeq seqLogo shannon.entropy showAsCell SitePairSet SitePairSetList SiteSet SiteSetList sitesSeq start storeMatrix tags TFFMDetail TFFMFirst toICM toPWM totalIC views writeGFF2 writeGFF3 XMatrixList

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cigarillo cli codetools cpp11 crayon curl DBI DelayedArray DirichletMultinomial fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue gtools httr IRanges jsonlite lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig pwalign R6 Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo seqLogo snow SparseArray SummarizedExperiment sys TFMPvalue vctrs XML XVector yaml

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

Rendered fromTFBSTools.Rmdusingknitr::rmarkdown

Last update: 2025-03-12
Started: 2015-11-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TFBS software package.	TFBSTools
calConservation method	calConservation calConservation,character,character-method calConservation,character,missing-method calConservation,DNAString,DNAString-method calConservation,DNAStringSet,missing-method calConservation-methods
JASPAR database operations	deleteMatrixHavingID deleteMatrixHavingID,character-method deleteMatrixHavingID,JASPAR2014-method deleteMatrixHavingID,JASPAR2016-method deleteMatrixHavingID,JASPAR2018-method deleteMatrixHavingID,JASPAR2020-method deleteMatrixHavingID,JASPAR2022-method deleteMatrixHavingID,SQLiteConnection-method initializeJASPARDB initializeJASPARDB,character-method initializeJASPARDB,JASPAR2014-method initializeJASPARDB,JASPAR2016-method initializeJASPARDB,JASPAR2018-method initializeJASPARDB,JASPAR2020-method initializeJASPARDB,JASPAR2022-method initializeJASPARDB,SQLiteConnection-method storeMatrix storeMatrix,character,PFMatrix-method storeMatrix,character,PFMatrixList-method storeMatrix,JASPAR2014,PFMatrix-method storeMatrix,JASPAR2014,PFMatrixList-method storeMatrix,JASPAR2016,PFMatrix-method storeMatrix,JASPAR2016,PFMatrixList-method storeMatrix,JASPAR2018,PFMatrix-method storeMatrix,JASPAR2018,PFMatrixList-method storeMatrix,JASPAR2020,PFMatrix-method storeMatrix,JASPAR2020,PFMatrixList-method storeMatrix,JASPAR2022,PFMatrix-method storeMatrix,JASPAR2022,PFMatrixList-method storeMatrix,SQLiteConnection,PFMatrix-method storeMatrix,SQLiteConnection,PFMatrixList-method storeMatrix-methods
dmmEM method	dmmEM dmmEM,ANY-method dmmEM,matrix-method dmmEM,PFMatrixList-method dmmEM-methods
Get the emission distribution parameters.	getEmissionProb getEmissionProb,TFFMDetail-method getEmissionProb,TFFMFirst-method
Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'	getMatrixByID getMatrixByID,character-method getMatrixByID,JASPAR2014-method getMatrixByID,JASPAR2016-method getMatrixByID,JASPAR2018-method getMatrixByID,JASPAR2020-method getMatrixByID,JASPAR2022-method getMatrixByID,SQLiteConnection-method getMatrixByName getMatrixByName,character-method getMatrixByName,JASPAR2014-method getMatrixByName,JASPAR2016-method getMatrixByName,JASPAR2018-method getMatrixByName,JASPAR2020-method getMatrixByName,JASPAR2022-method getMatrixByName,SQLiteConnection-method
Advanced JASPAR database search functions 'get_MatrixSet'	getMatrixSet getMatrixSet,character-method getMatrixSet,JASPAR2014-method getMatrixSet,JASPAR2016-method getMatrixSet,JASPAR2018-method getMatrixSet,JASPAR2020-method getMatrixSet,JASPAR2022-method getMatrixSet,SQLiteConnection-method
Get the emission probabilities of nucleotides	getPosProb getPosProb,TFFMDetail-method getPosProb,TFFMFirst-method
IUPAC2Matrix	IUPAC2Matrix
Some example PFM matrices.	MA0003.2 MA0004.1 MA0043 MA0048
Generate "FlatFileDir" directory	makeFlatFileDir
Class '"MotifSet"'	consensusMatrix,MotifSet-method length,MotifSet-method MotifSet MotifSet-class sitesSeq sitesSeq,MotifSet-method [,MotifSet,ANY,ANY,ANY-method [,MotifSet,ANY,ANY-method [,MotifSet-method
parseMEMEOutput	parseMEMEOutput
permuteMatrix method	permuteMatrix permuteMatrix,matrix-method permuteMatrix,PFMatrix-method permuteMatrix,PFMatrixList-method permuteMatrix-methods
PFMSimilarity method	PFMSimilarity PFMSimilarity,matrix,character-method PFMSimilarity,matrix,matrix-method PFMSimilarity,matrix,PFMatrix-method PFMSimilarity,PFMatrix,character-method PFMSimilarity,PFMatrix,matrix-method PFMSimilarity,PFMatrix,PFMatrix-method PFMSimilarity,PFMatrixList,character-method PFMSimilarity,PFMatrixList,matrix-method PFMSimilarity,PFMatrixList,PFMatrix-method PFMSimilarity-methods
PWMSimilarity method	PWMSimilarity PWMSimilarity,matrix,matrix-method PWMSimilarity,matrix,PWMatrix-method PWMSimilarity,PWMatrix,matrix-method PWMSimilarity,PWMatrix,PWMatrix-method PWMSimilarity,PWMatrixList,matrix-method PWMSimilarity,PWMatrixList,PWMatrix-method PWMSimilarity,PWMatrixList,PWMatrixList-method PWMSimilarity-methods
Read JASPAR format matrix	readJASPARMatrix
readXMLTFFM	readXMLTFFM
rPWMDmm method	rPWMDmm rPWMDmm,matrix-method rPWMDmm,PFMatrix-method rPWMDmm,PFMatrixList-method rPWMDmm-methods
Wrapper function for MEME	runMEME runMEME,character-method runMEME,DNAStringSet-method
sampleRanges	sampleRanges
searchAln method	searchAln searchAln,PWMatrix,Axt,missing-method searchAln,PWMatrix,character,character-method searchAln,PWMatrix,character,missing-method searchAln,PWMatrix,DNAString,DNAString-method searchAln,PWMatrix,DNAStringSet,missing-method searchAln,PWMatrixList,character,character-method searchAln,PWMatrixList,character,missing-method searchAln,PWMatrixList,DNAString,DNAString-method searchAln,PWMatrixList,DNAStringSet,missing-method
searchPairBSgenome method	searchPairBSgenome searchPairBSgenome,PWMatrix-method searchPairBSgenome,PWMatrixList-method searchPairBSgenome-methods
searchSeq method	searchSeq searchSeq,PWMatrix-method searchSeq,PWMatrixList-method searchSeq-methods
Plot a sequence logo	seqLogo seqLogo,ICMatrix-method seqLogo,TFFM-method
Calculate the Shannon entropy	shannon.entropy
Class '"SitePairSet"'	as.data.frame,SitePairSet-method length,SitePairSet-method site1,SitePairSet-method site2,SitePairSet-method SitePairSet SitePairSet-class
Class '"SitePairSetList"'	as.data.frame,SitePairSetList-method SitePairSetList SitePairSetList-class
Class '"SiteSet"'	as.data.frame,SiteSet-method c,SiteSet-method c-methods end,SiteSet-method length,SiteSet-method pattern,SiteSet-method primary,SiteSet-method pvalues pvalues,SiteSet-method relScore relScore,SiteSet-method score,SiteSet-method seqname,SiteSet-method show,SiteSet-method SiteSet SiteSet-class sitesource,SiteSet-method start,SiteSet-method strand,SiteSet-method views views,SiteSet-method [,SiteSet,ANY,ANY,ANY-method [,SiteSet,ANY,ANY-method [,SiteSet-method
Class '"SiteSetList"'	as.data.frame,SiteSetList-method pvalues,SiteSetList-method relScore,SiteSetList-method SiteSetList SiteSetList-class
The TFFM class	ncol,TFFMDetail-method ncol,TFFMFirst-method TFFM TFFMDetail TFFMFirst totalIC,TFFM-method
toGRangesList function	toGRangesList toGRangesList,SitePairSetList,Axt-method toGRangesList-methods
toICM method	toICM toICM,character-method toICM,DNAStringSet-method toICM,matrix-method toICM,PFMatrix-method toICM,PFMatrixList-method
toPWM method	toPWM toPWM,character-method toPWM,DNAStringSet-method toPWM,matrix-method toPWM,PFMatrix-method toPWM,PFMatrixList-method
'writeGFF3', 'writeGFF2' functions	writeGFF2 writeGFF2,SitePairSet-method writeGFF2,SitePairSetList-method writeGFF2,SiteSet-method writeGFF2,SiteSetList-method writeGFF2-methods writeGFF3 writeGFF3,SitePairSet-method writeGFF3,SitePairSetList-method writeGFF3,SiteSet-method writeGFF3,SiteSetList-method writeGFF3-methods
'"XMatrix"' objects	as.matrix,XMatrix-method bg bg,XMatrix-method bg<-,XMatrix-method colSums,XMatrix-method dim,XMatrix-method ICMatrix ICMatrix-class ID ID,XMatrix-method ID<-,XMatrix-method length,XMatrix-method length-methods Matrix Matrix,XMatrix-method Matrix<- Matrix<-,XMatrix-method matrixClass matrixClass,XMatrix-method matrixClass<-,XMatrix-method matrixType matrixType,ICMatrix-method matrixType,PFMatrix-method matrixType,PWMatrix-method matrixType-methods name name,XMatrix-method name<-,XMatrix-method ncol,XMatrix-method PFMatrix PFMatrix-class PWMatrix PWMatrix-class reverseComplement,XMatrix-method rowSums,XMatrix-method strand,XMatrix-method strand<-,XMatrix-method tags tags,XMatrix-method totalIC totalIC,ICMatrix-method totalIC-methods XMatrix XMatrix-class [-methods
Class '"XMatrixList"'	bg,XMatrixList-method ICMatrixList ICMatrixList-class ID,XMatrixList-method Matrix,XMatrixList-method matrixClass,XMatrixList-method matrixType,XMatrixList-method name,XMatrixList-method PFMatrixList PFMatrixList-class PWMatrixList PWMatrixList-class showAsCell,XMatrixList-method strand,XMatrixList-method tags,XMatrixList-method XMatrixList XMatrixList,list-method