To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

TFBSTools

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see TFBSTools.

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Bioconductor version: 3.2

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites and transcription factor profile matrices.

Author: Ge Tan <ge.tan09 at imperial.ac.uk>

Maintainer: Ge Tan <ge.tan09 at imperial.ac.uk>

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")

 

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

Details

biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription
Version 1.8.3
In Bioconductor since BioC 2.13 (R-3.0) (2.5 years)
License GPL-2
Depends R (>= 3.2.2)
Imports Biostrings(>= 2.36.4), RSQLite (>= 1.0.0), seqLogo(>= 1.34.0), GenomicRanges(>= 1.20.6), caTools (>= 1.17.1), XVector(>= 0.8.0), rtracklayer(>= 1.28.10), BSgenome(>= 1.36.3), S4Vectors(>= 0.6.5), IRanges(>= 2.2.7), methods, gtools (>= 3.5.0), CNEr(>= 1.4.0), BiocParallel(>= 1.2.21), DirichletMultinomial(>= 1.10.0), TFMPvalue (>= 0.0.5), BiocGenerics(>= 0.14.0), XML (>= 3.98-1.3), grid, Biobase(>= 2.28), GenomeInfoDb(>= 1.6.1)
LinkingTo
Suggests JASPAR2014(>= 1.4.0), RUnit (>= 0.4.29), BiocStyle(>= 1.7.7), knitr (>= 1.11)
SystemRequirements
Enhances
URL https://bitbucket.org/ge11232002/tfbstools
BugReports https://bitbucket.org/ge11232002/tfbstools/issues
Depends On Me
Imports Me MatrixRider
Suggests Me
Build Report  

Package Archives

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

Package Source TFBSTools_1.8.3.tar.gz
Windows Binary TFBSTools_1.8.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) TFBSTools_1.8.0.tgz
Mac OS X 10.9 (Mavericks) TFBSTools_1.8.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TFBSTools/tree/release-3.2
Package Short Url http://bioconductor.org/packages/TFBSTools/
Package Downloads Report Download Stats

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