ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be appli...
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| Published in: | Molecular bioSystems Vol. 12; no. 2; p. 477 |
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| Main Authors: | , |
| Format: | Journal Article |
| Language: | English |
| Published: |
England
01-01-2016
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| Online Access: | Get more information |
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| Abstract | Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA). |
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| AbstractList | Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. A functional analysis can be applied to the genomic coordination obtained from a sequencing experiment to analyze the functional significance of genomic loci including cis-regulatory elements and non-coding regions. Comparison among different experiments is also supported. Moreover, ReactomePA provides several visualization functions to produce highly customizable, publication-quality figures. The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packages/ReactomePA). |
| Author | He, Qing-Yu Yu, Guangchuang |
| Author_xml | – sequence: 1 givenname: Guangchuang surname: Yu fullname: Yu, Guangchuang email: tqyhe@jnu.edu.cn organization: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn and State Key Laboratory of Emerging Infectious Disease, School of Public Health, The University of Hong Kong, Hong Kong SAR, China – sequence: 2 givenname: Qing-Yu surname: He fullname: He, Qing-Yu email: tqyhe@jnu.edu.cn organization: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China. tqyhe@jnu.edu.cn |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26661513$$D View this record in MEDLINE/PubMed |
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