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 3.4 of Bioconductor; for the stable, up-to-date release version, see TFBSTools.

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Bioconductor version: 3.4

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

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 1.12.2

In Bioconductor since BioC 2.13 (R-3.0) (3.5 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, JASPAR2016(>= 1.0.0)

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