cobindR

DOI: 10.18129/B9.bioc.cobindR    

This package is for version 3.10 of Bioconductor; for the 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 (!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 1.24.0
In Bioconductor since BioC 2.13 (R-3.0) (6.5 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_1.24.0.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
Package Short Url https://bioconductor.org/packages/cobindR/
Package Downloads Report Download Stats

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