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. 2012 May;16(5):284-7.
doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28.

clusterProfiler: an R package for comparing biological themes among gene clusters

Guangchuang Yu  1 , Li-Gen Wang, Yanyan Han, Qing-Yu He
Affiliations

clusterProfiler: an R package for comparing biological themes among gene clusters

Guangchuang Yu et al. OMICS. 2012 May.

Abstract

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

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Figures

FIG. 1.
FIG. 1.
Comparison of GO enrichment of gene clusters.
See this image and copyright information in PMC

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References

    1. Ashburner M. Ball C.A. Blake J.A. Botstein D. Butler H. Cherry J.M., et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–29. - PMC - PubMed
    1. Asur S. Ucar D. Parthasarathy S. An ensemble framework for clustering protein–protein interaction networks. Bioinformatics. 2007;23:i29–i40. - PubMed
    1. Bindea G. Mlecnik B. Hackl H. Charoentong P. Tosolini M. Kirilovsky A., et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091–1093. - PMC - PubMed
    1. Boyle E.I. Weng S. Gollub J. Jin H. Botstein D. Cherry J.M., et al. GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004;20:3710–3715. - PMC - PubMed
    1. Falcon S. Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007;23:257–258. - PubMed

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