MotIV

DOI: 10.18129/B9.bioc.MotIV    

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

Motif Identification and Validation

Bioconductor version: 3.8

This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

Author: Eloi Mercier, Raphael Gottardo

Maintainer: Eloi Mercier <emercier at bcgsc.ca>, Raphael Gottardo <rgottard at fhcrc.org>

Installation

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

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

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("MotIV")

 

PDF	R Script	The MotIV users guide
PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, GenomicSequence, Microarray, MotifAnnotation, Software
Version	1.38.0
In Bioconductor since	BioC 2.6 (R-2.11) (9 years)
License	GPL-2
Depends	R (>= 2.10), BiocGenerics(>= 0.1.0)
Imports	graphics, grid, methods, S4Vectors, IRanges(>= 1.13.5), Biostrings(>= 1.24.0), lattice, rGADEM, utils
LinkingTo
Suggests	rtracklayer
SystemRequirements	GNU Scientific Library >= 1.6 (http://www.gnu.org/software/gsl/)
Enhances
URL
Depends On Me	motifStack
Imports Me	TCGAWorkflow
Suggests Me	universalmotif
Links To Me
Build Report

Package Archives

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

Source Package	MotIV_1.38.0.tar.gz
Windows Binary	MotIV_1.38.0.zip
Mac OS X 10.11 (El Capitan)	MotIV_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MotIV
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MotIV
Package Short Url	http://bioconductor.org/packages/MotIV/
Package Downloads Report	Download Stats