motifRG statistics

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Citations per year

Number of citations per year for the bioinformatics software tool motifRG
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Tool usage distribution map

This map represents all the scientific publications referring to motifRG per scientific context
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motifRG specifications

Information


Unique identifier OMICS_00487
Name motifRG
Software type Package/Module
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 1.24.0
Stability Stable
Requirements
methods, parallel, grid, graphics, IRanges, Biostrings, R(>=2.15), Biostrings(>=2.26), seqLogo, BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19
Maintained Yes

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Publication for motifRG

motifRG citations

 (3)
library_books

Direct AUC optimization of regulatory motifs

2017
Bioinformatics
PMCID: 5870558
PMID: 28881989
DOI: 10.1093/bioinformatics/btx255

[…] ch for motif directly over the complete parameter space, but instead adopt approximate schemes that could sacrifice both accuracy and expressive power. For example, the motifs learned by DREME () and MotifRG () are limited to the discrete IUPAC space, while HOMER () chooses to refine motifs by only tuning external parameters. Therefore, although DML algorithms could rapidly identify binding motifs […]

library_books

Intrinsic Epigenetic Regulation of the D4Z4 Macrosatellite Repeat in a Transgenic Mouse Model for FSHD

2013
PLoS Genet
PMCID: 3616921
PMID: 23593020
DOI: 10.1371/journal.pgen.1003415

[…] age, which models background reads by a negative binomial distribution as previously described . To identify the DUX4 consensus binding sequence, we applied an in-house developed Bioconductor package motifRG for discriminative de novo motif discovery as previously described , .For supporting concerning supplemental data, please refer to . […]

library_books

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors

2012
PLoS Genet
PMCID: 3355086
PMID: 22615585
DOI: 10.1371/journal.pgen.1002728

[…] The R-package motifRG (Bioconductor package motifRG, Zizhen Yao, manuscript in preparation) was used to identify binding motifs, using sequences +/−100 bp around the summit of the top 300 highest ranking peaks. Unr […]


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motifRG institution(s)
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, School of Medicine, Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Computer Science and Engineering, Department of Genome Sciences, University of Washington, Seattle, WA, USA; Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
motifRG funding source(s)
Supported by Interdisciplinary Training Program grant [T32 CA080416]; Developmental Biology Predoctoral Training Grant [T32HD007183]; and. National Institutes of Health NIAMS [R01AR045113].

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