clusterProfiler : an R Package for Comparing Biological Themes Among Gene Clusters

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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.

Salvato in:
Autori: Guangchuang Yu iD (Jinan University); Li-Gen Wang; Yanyan Han iD (Jinan University); Qing‐Yu He iD (Jinan University)
Pubblicato in: OMICS A Journal of Integrative Biology, vol. 16, n. 5, pp. 284-287
Data di pubblicazione:28/03/2012
Editore:Mary Ann Liebert, Inc.
Tipo di documento:Articolo
Lingua:inglese
DOI: 10.1089/omi.2011.0118
ISSN:1536-2310, 1557-8100
Accesso aperto: Accesso aperto Green: copia in un archivio istituzionale o disciplinare – PubMed Central
Citazioni ricevute:36.126
Soggetti:
Bioinformatics and Genomic Networks (Life Sciences > Biochemistry, Genetics and Molecular Biology > Molecular Biology)
Genomics and Phylogenetic Studies (Life Sciences > Biochemistry, Genetics and Molecular Biology > Molecular Biology)
Biomedical Text Mining and Ontologies (Life Sciences > Biochemistry, Genetics and Molecular Biology > Molecular Biology)
gene clusters, transcriptomics, proteomics, R package, Bioconductor, ontology annotation
Identificativi: OpenAlex W2035618305 · PMID 22455463

Dati dell'indice centrale: OpenAlex (licenza CC0).

Riassunto: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.
ISSN:1536-2310
1557-8100
DOI:10.1089/omi.2011.0118