RevEcoR: Reverse Ecology Analysis on Microbiome

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.

AuthorYang Cao, Fei Li
Date of publication2016-04-03 17:14:01
MaintainerYang Cao <>
LicenseGPL (>= 2)

View on CRAN


\%.\% Man page
anno.species Man page
calculateCooperationIndex Man page
competitionIndex Man page
complementarityIndex Man page
compose Man page
confidencescore Man page
confidencescore-methods Man page
confidencescore,seedset-method Man page
getGsMN Man page
getGsMN-methods Man page
getGsMN,seedset-method Man page
getOrgMetabolicData Man page
getSeedSets Man page
gut_microbiome Man page
Interactions Man page
kegg_buc Man page
kegg_ptr Man page
KosarajuSCC Man page
len Man page
len-methods Man page
len,seedset-method Man page
nonseed Man page
nonseed-methods Man page
nonseed,seedset-method Man page
reconstructGsMN Man page
RefDbcache Man page
RevEcoR Man page
RevEcoR-package Man page
seedset-class Man page
seedSize Man page
seedSize-methods Man page
seedSize,seedset-method Man page
show Man page
show-methods Man page
show,seedset-method Man page

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.