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

DOI: 10.18129/B9.bioc.cobindR

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

Need some help? Ask on the Bioconductor Support site!

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

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