A metagenomic pipeline for systems biology

Bioconductor version: Release (2.14)

This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.

Author: Yang Cao, Fei Li

Maintainer: Yang Cao <yiluheihei at>, Fei Li <pittacus at>

To install this package, start R and enter:


Citation (from within R, enter citation("mmnet")):


PDF R Script mmnet
PDF   Reference Manual


biocViews GraphsAndNetwork, Microbiome, Pathways, Sequencing, Software, SystemsBiology
Version 1.2.2
In Bioconductor since BioC 2.14 (R-3.1)
License GPL (>= 2)
Depends R (>= 2.14), igraph, biom
Imports Biobase, RJSONIO, stringr, reshape2, ggplot2, KEGGREST, plyr, XML, RCurl, flexmix, Matrix, methods, tools
Suggests RCytoscape, graph, knitr
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source mmnet_1.2.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) mmnet_1.2.2.tgz
Mac OS X 10.9 (Mavericks) mmnet_1.2.2.tgz
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