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rGADEM specifications

Information


Unique identifier OMICS_00491
Name rGADEM
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.28.0
Stability Stable
Requirements
methods, graphics, IRanges, Biostrings, seqLogo, BSgenome, BSgenome.Hsapiens.UCSC.hg19, R(>=2.11.0)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Raphael Gottardo

Publication for rGADEM

rGADEM citations

 (4)
library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] ion or learning of the motif in the gap positions between the dimer components. MODER can be seen as a generalization of coMOTIF. Recent EM algorithm based finders of monomer motifs include GADEM and rGADEM (,) which use genetic algorithm with EM to improve starting PPMs, SEME () which uses importance sampling to speed-up the search, EXTREME () which achieves speed-up by using the on–line version […]

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

[…] R.UTF–8 LC _ IDENTIFICATION= C 12 13 attached base packages : 14 [1] stats4 parallel grid stats graphics grDevices utils 15 [8] datasets methods base 16 17 other attached packages : 18 [1] rGADEM _ 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 […]

library_books

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays

2016
Front Plant Sci
PMCID: 5031598
PMID: 27713757
DOI: 10.3389/fpls.2016.01433

[…] sequence GVSGRSGNSGRSGVSGRSG (He et al., in review). The motif was identified from ∼900 genic hotspot regions that did not contain transposable elements. Copies of the motif were identified using the rGADEM package () to re-scan these genic hotspot regions for matches to the position weight matrix of the motif using a stringency of 80%. […]

library_books

Nrf2 suppresses macrophage inflammatory response by blocking proinflammatory cytokine transcription

2016
Nat Commun
PMCID: 4879264
PMID: 27211851
DOI: 10.1038/ncomms11624

[…] nner. Peaks were annotated with BEDtools and a ChIPpeakAnno package (ver. 2.10.0). For the de novo motif discovery, the sequences of the −25-bp to +25-bp region from peak summits were analysed with a rGADEM package (ver. 2.0.10, Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li (2014). rGADEM: de novo motif discovery). […]

Citations

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rGADEM 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, QC, Canada; Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, 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
rGADEM 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); by The Network of Applied Genetic Medicine (RMGA); and 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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