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rGADEM

A package containing an extended version of the original GADEM C code. For ChIP-Seq data, a key improvement is that, on multicore computers, rGADEM can take advantage of multithreading via Grand Central Dispatch on Mac OS X 10.6 and above, and openMP on other Unix platforms, to sharply reduce run times. It can also prioritize sequences with large ChIP enrichments and includes novel prior distributions that prioritize for motif occurrences that are nearer to sequence (peak) centers. Such prior settings can potentially improve the detection of primary motifs at the cost of missing secondary motifs that can be present at low enrichment and/or further away for the center. rGADEM is an efficient motif discovery tool for large-scale genomic sequence data. It provides a complete set of Bioconductor tools for sequence and motif analysis of ChIP-seq and ChIP-chip data.

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rGADEM classification

rGADEM specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
2.20.0
Requirements:
Biostrings, IRanges, BSgenome, methods, seqLogo

rGADEM distribution

versioning

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rGADEM support

Documentation

Credits

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Publications

Institution(s)

Computational Biology Unit, Institut de Recherche Clinique de Montreal, Montreal, 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, Canada; Department of Statistics, University of British Columbia, Vancouver, Canada; Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Funding source(s)

National Institutes of Health (NIH) grant no. R01-HG005692; Intramural Research Program of the NIH (in part); National Institute of Environmental Health Sciences (ES101765-05); The Network of Applied Genetic Medicine (RMGA); the MORGEN (Dissecting Gene Expression Networks in Mammalian Organogenesis) project

Link to literature

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