cobindR

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cobindR.

Finding Co-occuring motifs of transcription factor binding sites


Bioconductor version: 3.10

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>

Citation (from within R, enter citation("cobindR")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
Using cobindR PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBiology, ChIPSeq, MultipleComparison, SequenceMatching, Software
Version 1.24.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-2.0
Depends
Imports methods, seqinr, yaml, rtfbs, gplots, mclust, gmp, BiocGenerics(>= 0.13.8), IRanges, Biostrings, BSgenome, biomaRt
System Requirements
URL
See More
Suggests RUnit
Linking To
Enhances rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cobindR_1.24.0.tar.gz
Windows Binary cobindR_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cobindR_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cobindR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cobindR
Bioc Package Browser https://code.bioconductor.org/browse/cobindR/
Package Short Url https://bioconductor.org/packages/cobindR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive