cobindR

DOI: 10.18129/B9.bioc.cobindR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see cobindR.

Finding Co-occuring motifs of transcription factor binding sites

Bioconductor version: 3.8

Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes

Author: Manuela Benary, Stefan Kroeger, Yuehien Lee, Robert Lehmann

Maintainer: Manuela Benary <manuela.benary at cms.hu-berlin.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cobindR")

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("cobindR")

 

PDF	R Script	Using cobindR
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, ChIPSeq, MultipleComparison, SequenceMatching, Software
Version	1.20.0
In Bioconductor since	BioC 2.13 (R-3.0) (5.5 years)
License	Artistic-2.0
Depends
Imports	methods, seqinr, yaml, rtfbs, gplots, mclust, gmp, BiocGenerics(>= 0.13.8), IRanges, Biostrings, BSgenome, biomaRt
LinkingTo
Suggests	RUnit
SystemRequirements
Enhances	rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cobindR_1.20.0.tar.gz
Windows Binary	cobindR_1.20.0.zip
Mac OS X 10.11 (El Capitan)	cobindR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cobindR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cobindR
Package Short Url	http://bioconductor.org/packages/cobindR/
Package Downloads Report	Download Stats