Reverse Ecology Analysis on Microbiome
Calculating the metabolic competition and complementarity index
Compose multiple functions
Conficence score
The genome scale metabolic network
Get organism metabolic data from KEGG database
Identify seed compounds of each organism
Calculating the species interactions
Caculating the strong connected components (SCC) of a network
the length of the seed set
Non seed of the network
Reconstuction of the specific-organism genome-scale metabolic network
The RevEcoR package
seedset-class
Size of the each seed source component
The show generic function
An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.