TFBSTools

This is the development version of TFBSTools; for the stable release version, see TFBSTools.

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.39.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 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
Linking To
Suggests	BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown
System Requirements
Enhances
URL	https://github.com/ge11232002/TFBSTools
Bug Reports	https://github.com/ge11232002/TFBSTools/issues

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

Package Archives

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

Source Package	TFBSTools_1.39.0.tar.gz
Windows Binary	TFBSTools_1.39.0.zip
macOS Binary (x86_64)	TFBSTools_1.39.0.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