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chevron_left Data analysis De novo motif discovery chevron_right
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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


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Documentation


Maintainer


  • person_outline Raphael Gottardo <>

Publication for rGADEM

rGADEM in pipelines

 (2)
2015
PMCID: 4352986
PMID: 25633350
DOI: 10.1242/dev.116996

[…] pancrnas in 2-cell embryos were selected by comparing their levels with those in mii oocytes. the −200 to −1 bp sequences (relative to the tss) of 370 corresponding mrnas were examined using rgadem, one of the bioconductor packages (). to verify the presence of a motif in the pancrna-partnered gene loci, we further extracted and counted genes that possessed or lacked sequences showing […]

2014
PMCID: 3898825
PMID: 24438357
DOI: 10.1186/1471-2164-15-35

[…] to −1 bp) of the candidate pancrna-bearing genes. in this analysis, we defined an orf as a region which begins with a start codon and ends with a stop codon., for motif discovery, we employed the rgadem package (v.1.0.1) [], which is available through bioconductor [], with the default parameter (p-value < 0.0002) [] with dna sequences from −1,000 bp to +1,000 bp relative to tsss […]


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rGADEM in publications

 (6)
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] 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 […]

PMCID: 5459992
PMID: 28556835
DOI: 10.1038/ncomms15527

[…] conversion rate was estimated by calculating the c to t conversion at non-cpg sites. differential methylation region was calculated with biseq. dmrs were considered significant with p<0.05. rgadem was used for unseeded motif analysis with default settings and motiv for e value calculation and visualization based on jaspar 2010 scores. euclidean-based multidimensional scaling and dna […]

PMCID: 5031598
PMID: 27713757
DOI: 10.3389/fpls.2016.01433

[…] 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%., gc, gc1, gc2, and gc3 were calculated using custom perl […]

PMCID: 4879264
PMID: 27211851
DOI: 10.1038/ncomms11624

[…] 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)., bmdms were incubated with 5-ng ml−1 lps and 100-μg ml−1 alum […]

PMCID: 4352986
PMID: 25633350
DOI: 10.1242/dev.116996

[…] pancrnas in 2-cell embryos were selected by comparing their levels with those in mii oocytes. the −200 to −1 bp sequences (relative to the tss) of 370 corresponding mrnas were examined using rgadem, one of the bioconductor packages (). to verify the presence of a motif in the pancrna-partnered gene loci, we further extracted and counted genes that possessed or lacked sequences showing […]


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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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