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Bioinformatics. 2011 Jul 1;27(13):1882-3. doi: 10.1093/bioinformatics/btr296. Epub 2011 May 10.

Model-based gene set analysis for Bioconductor.

Author information

1
Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

Abstract

Gene Ontology and other forms of gene-category analysis play a major role in the evaluation of high-throughput experiments in molecular biology. Single-category enrichment analysis procedures such as Fisher's exact test tend to flag large numbers of redundant categories as significant, which can complicate interpretation. We have recently developed an approach called model-based gene set analysis (MGSA), that substantially reduces the number of redundant categories returned by the gene-category analysis. In this work, we present the Bioconductor package mgsa, which makes the MGSA algorithm available to users of the R language. Our package provides a simple and flexible application programming interface for applying the approach.

AVAILABILITY:

The mgsa package has been made available as part of Bioconductor 2.8. It is released under the conditions of the Artistic license 2.0.

CONTACT:

peter.robinson@charite.de; julien.gagneur@embl.de.

PMID:
21561920
PMCID:
PMC3117381
DOI:
10.1093/bioinformatics/btr296
[Indexed for MEDLINE]
Free PMC Article
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