mmnet: An R Package for Metagenomics Systems Biology Analysis.
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 c...
| Publicado en: | BioMed Research International Vol. 2015; pp. 1 - 6 |
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| Autores principales: | , , , |
| Formato: | Journal Article |
| Publicado: |
Wiley-Blackwell
9/3/2015
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109471199&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109471199 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 9/3/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109471199 109471199 NLM26421278 10.1155/2015/167249 NLM26421278 PMC4573221 109471199 ppf: 1 ppct: 5 formats: fmt: @attributes: type: P tig: atl: mmnet: An R Package for Metagenomics Systems Biology Analysis. aug: au: Cao, Yang Zheng, Xiaofei Li, Fei Bo, Xiaochen affil: Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing 100850, China sug: ab: 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. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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