Package: TFBSTools 1.45.0

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]

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TFBSTools.pdf |TFBSTools.html✨
TFBSTools/json (API)
NEWS

# 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-1.45.0(bioc 3.21)TFBSTools-1.44.0(bioc 3.20)

motifannotation generegulation motifdiscovery transcription alignment

11.99 score 25 stars 18 packages 984 scripts 7.0k downloads 33 mentions 68 exports 116 dependencies

Last updated 25 days agofrom:58fd543eab. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	WARNING	Oct 31 2024
R-4.4-mac-x86_64	WARNING	Oct 31 2024
R-4.4-mac-aarch64	NOTE	Oct 31 2024
R-4.3-win-x86_64	WARNING	Oct 31 2024
R-4.3-mac-x86_64	WARNING	Oct 31 2024
R-4.3-mac-aarch64	NOTE	Oct 31 2024

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 toGRangesList toICM toPWM totalIC views writeGFF2 writeGFF3 XMatrixList

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cli clipr CNEr codetools colorspace cpp11 crayon curl DBI DelayedArray DirichletMultinomial fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales seqLogo snow SparseArray stringi stringr SummarizedExperiment sys TFMPvalue tibble tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xtable XVector yaml zlibbioc

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

Ge Tan

Rendered fromTFBSTools.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-03-11
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