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TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis


Bioconductor version: Release (3.18)

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.

Author: Ge Tan [aut, cre]

Maintainer: Ge Tan <ge_tan at live.com>

Citation (from within R, enter citation("TFBSTools")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TFBSTools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TFBSTools")
Transcription factor binding site (TFBS) analysis with the "TFBSTools" package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription
Version 1.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.2.2)
Imports Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools (>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools (>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite (>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3), XVector(>= 0.8.0), parallel
System Requirements
URL https://github.com/ge11232002/TFBSTools
Bug Reports https://github.com/ge11232002/TFBSTools/issues
See More
Suggests BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me ATACCoGAPS, ATACseqTFEA, chromVAR, enrichTF, esATAC, MatrixRider, monaLisa, motifmatchr, motifStack, primirTSS, spatzie
Suggests Me CAGEWorkflow, enhancerHomologSearch, GRaNIE, JASPAR2018, JASPAR2020, JASPAR2022, MAGAR, MethReg, pageRank, universalmotif
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TFBSTools_1.40.0.tar.gz
Windows Binary TFBSTools_1.40.0.zip
macOS Binary (x86_64) TFBSTools_1.40.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/TFBSTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TFBSTools
Bioc Package Browser https://code.bioconductor.org/browse/TFBSTools/
Package Short Url https://bioconductor.org/packages/TFBSTools/
Package Downloads Report Download Stats