TFBSTools

DOI: 10.18129/B9.bioc.TFBSTools    

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TFBSTools")

Documentation

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

browseVignettes("TFBSTools")

 

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

Details

biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription
Version 1.18.0
In Bioconductor since BioC 2.13 (R-3.0) (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
LinkingTo
Suggests BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016(>= 1.0.0)
SystemRequirements
Enhances
URL https://github.com/ge11232002/TFBSTools
BugReports https://github.com/ge11232002/TFBSTools/issues
Depends On Me
Imports Me chromVAR, esATAC, MatrixRider, motifmatchr
Suggests Me JASPAR2018, JASPAR2018
Links To Me
Build Report  

Package Archives

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

Source Package TFBSTools_1.18.0.tar.gz
Windows Binary TFBSTools_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) TFBSTools_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TFBSTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TFBSTools
Package Short Url http://bioconductor.org/packages/TFBSTools/
Package Downloads Report Download Stats

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