mmnet: Metagenomic analysis of microbiome metabolic network

2 Analysis Pipeline: from raw Metagenomic Sequence Data to Metabolic Network Analysis 2 2.1 Prepare metagenomic sequence data . . . . . . . . . . . . . . . . . . 3 2.2 Annotation of Metagenomic Sequence Reads . . . . . . . . . . . . . 3 2.3 Estimating the abundance of enzymatic genes . . . . . . . . . . . . . 5 2.4 Building reference metabolic dataset . . . . . . . . . . . . . . . . . . 7 2.5 Constructing State Specific Network . . . . . . . . . . . . . . . . . . 8 2.6 Topological network analysis . . . . . . . . . . . . . . . . . . . . . . 9 2.7 Differential network analysis . . . . . . . . . . . . . . . . . . . . . . 10 2.8 Network Visualization . . . . . . . . . . . . . . . . . . . . . . . . . 10