MotIV

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MotIV.

Motif Identification and Validation


Bioconductor version: 3.9

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>

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

Installation

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


if (!require("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")
The MotIV users guide PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, ChIPchip, GenomicSequence, Microarray, MotifAnnotation, Software
Version 1.40.0
In Bioconductor since BioC 2.6 (R-2.11) (14 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
System Requirements GNU Scientific Library >= 1.6 (http://www.gnu.org/software/gsl/)
URL
See More
Suggests rtracklayer
Linking To
Enhances
Depends On Me motifStack
Imports Me TCGAWorkflow
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MotIV_1.40.0.tar.gz
Windows Binary MotIV_1.40.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MotIV_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MotIV
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MotIV
Bioc Package Browser https://code.bioconductor.org/browse/MotIV/
Package Short Url https://bioconductor.org/packages/MotIV/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive