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 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 (3.3)

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.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")

 

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

Details

biocViews Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription
Version 1.9.11
In Bioconductor since BioC 2.13 (R-3.0) (2.5 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, 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)
LinkingTo
Suggests BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat
SystemRequirements
Enhances
URL https://github.com/ge11232002/TFBSTools
BugReports https://github.com/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_1.9.11.tar.gz
Windows Binary TFBSTools_1.9.11.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) TFBSTools_1.7.1.tgz
Mac OS X 10.9 (Mavericks) TFBSTools_1.9.11.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/TFBSTools
Package Short Url http://bioconductor.org/packages/TFBSTools/
Package Downloads Report Download Stats

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