mmnet: An R Package for Metagenomics Systems Biology Analysis
Joint Authors
Cao, Yang
Zheng, Xiaofei
Li, Fei
Bo, Xiaochen
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-5, 5 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-09-03
Country of Publication
Egypt
No. of Pages
5
Main Subjects
Abstract EN
The human microbiome plays important roles in human health and disease.
Previous microbiome studies focused mainly on single pure species function and overlooked the interactions in the complex communities on system-level.
A metagenomic approach introduced recently integrates metagenomic data with community-level metabolic network modeling, but no comprehensive tool was available for such kind of approaches.
To facilitate these kinds of studies, we developed an R package, mmnet, to implement community-level metabolic network reconstruction.
The package also implements a set of functions for automatic analysis pipeline construction including functional annotation of metagenomic reads, abundance estimation of enzymatic genes, community-level metabolic network reconstruction, and integrated network analysis.
The result can be represented in an intuitive way and sent to Cytoscape for further exploration.
The package has substantial potentials in metagenomic studies that focus on identifying system-level variations of human microbiome associated with disease.
American Psychological Association (APA)
Cao, Yang& Zheng, Xiaofei& Li, Fei& Bo, Xiaochen. 2015. mmnet: An R Package for Metagenomics Systems Biology Analysis. BioMed Research International،Vol. 2015, no. 2015, pp.1-5.
https://search.emarefa.net/detail/BIM-1054452
Modern Language Association (MLA)
Cao, Yang…[et al.]. mmnet: An R Package for Metagenomics Systems Biology Analysis. BioMed Research International No. 2015 (2015), pp.1-5.
https://search.emarefa.net/detail/BIM-1054452
American Medical Association (AMA)
Cao, Yang& Zheng, Xiaofei& Li, Fei& Bo, Xiaochen. mmnet: An R Package for Metagenomics Systems Biology Analysis. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-5.
https://search.emarefa.net/detail/BIM-1054452
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1054452