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MotIV specifications

Information


Unique identifier OMICS_28133
Name MotIV
Alternative name Motif Identification and Validation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.36.0
Stability Stable
Requirements
methods, grid, graphics, utils, S4Vectors, rtracklayer, lattice, R(>=2.10), BiocGenerics(>=0.1.0), IRanges(>=1.13.5), Biostrings(>=1.24.0), rGADEM
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Raphael Gottardo

Publication for Motif Identification and Validation

MotIV citations

 (4)
library_books

Maser: one stop platform for NGS big data from analysis to visualization

2018
PMCID: 5905357
PMID: 29688385
DOI: 10.1093/database/bay027

[…] IP-seq category contains a single pipeline that executes the mapping with Bowtie2 (), peak calling with MACS (). The pipelines subsequently search binding motifs with GADEM for a de novo motif () and MotIV for a known motif () in the defined peaks, and the nearest neighbor gene to those motifs (annotation).The BS-seq category contains two pipelines that differ in the mapping tool they use: Bismark […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] 2.20.0 19 [2] seqLogo _ 1.38.0 20 [3] BSgenome _ 1.40.1 21 [4] rtracklayer _ 1.32.1 22 [5] motifStack _ 1.16.2 23 [6] ade4 _ 1.7–4 24 [7] grImport _ 0.9–0 25 [8] XML _ 3.98–1.4 26 [9] MotIV _ 1.28.0 27 [10] pathview _ 1.12.0 28 [11] biomaRt _ 2.28.0 29 [12] minet _ 3.30.0 30 [13] clusterProfiler _ 3.0.4 31 [14] DOSE _ 2.10.7 32 [15] AnnotationHub _ 2.4.2 33 [16] ChIPseeker _ […]

library_books

Lipid mediated regulation of SKN 1/Nrf in response to germ cell absence

2015
eLife
PMCID: 4541496
PMID: 26196144
DOI: 10.7554/eLife.07836.042

[…] annotations and phenotypes were obtained from WormBase build WS246. SKN-1 transcription factor binding site analysis of hits was conducted with biomaRt, GenomicFeatures, JASPAR, MotifDb, motifStack, MotIV, and Rsamtools (; , ; ; ; ; ). JASPAR analysis was performed with the SKN-1 matrix MA0547.1 using 2 kb upstream sequences obtained from Ensembl WBcel235 (). modENCODE SKN-1::GFP ChIP-seq analysi […]

library_books

Exploring the transcription factor activity in high throughput gene expression data using RLQ analysis

2013
BMC Bioinformatics
PMCID: 3686578
PMID: 23742070
DOI: 10.1186/1471-2105-14-178

[…] However, recent bioinformatic developments allow the automation of most of these complex processes. Several open-source applications were developed, including statistical packages (e.g. the R package MotIV []), as well as various web tools. As an example, Zambelli and collaborators [] recently proposed a new application — pscan — which facilitates the discovery of TFBSs, which are over- (or under- […]

Citations

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MotIV institution(s)
Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, QC, Canada; Department of Molecular Medecine, Faculty of Medicine, Endocrinology and Genomics, Centre de Recherche du CHUQ (CRCHUQ), Laval University, Quebec, QC, Canada; Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, USA; BC Cancer Agency, Genome Sciences Centre, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
MotIV funding source(s)
Supported by National Institutes of Health (NIH) grant no. R01-HG005692; by Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (ES101765-05); the Network of Applied Genetic Medicine (RMGA); by the MORGEN (Dissecting Gene Expression Networks in Mammalian Organogenesis) project, which was funded by Genome Canada, Genome British Columbia, the Heart and Stroke Foundation of BC/Yukon, the British Columbia Knowledge Development Fund, the Juvenile Diabetes Research Foundation, the Vancouver Foundation, the BC Cancer Foundation, and the Michael Smith Foundation for Health Research.

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