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>

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

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

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