# Reverse Ecology Analysis on Microbiome

## Documentation for package ‘RevEcoR’ version 0.99.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

RevEcoR-package | The RevEcoR package
%.% | Compose multiple functions
anno.species | Annotation profiles of seven well-studied oral species
calculateCooperationIndex | Calculating the metabolic competition and complementarity index
competitionIndex | Calculating the species interactions
complementarityIndex | Calculating the species interactions
compose | Compose multiple functions
confidencescore | Conficence score
confidencescore-method | Conficence score
confidencescore-methods | Conficence score
getGsMN | The genome scale metabolic network
getGsMN-method | The genome scale metabolic network
getGsMN-methods | The genome scale metabolic network
getOrgMetabolicData | Get organism metabolic data from KEGG database
getSeedSets | Identify seed compounds of each organism
gut_microbiome | Annotation profiles of 116 gut prevalent species
Interactions | Calculating the species interactions
kegg_buc | Metabolic profiles of KEGG organism Buchnera aphidicola APS (Acyrthosiphon pisum) (KEGG organism code: buc)
kegg_ptr | Metabolic profiles of KEGG organism Pan troglodytes (chimpanzee) (KEGG organism code: ptr)
KosarajuSCC | Caculating the strong connected components (SCC) of a network
len | the length of the seed set
len-method | the length of the seed set
len-methods | the length of the seed set
nonseed | Non seed of the network
nonseed-method | Non seed of the network
nonseed-methods | Non seed of the network
reconstructGsMN | Reconstuction of the specific-organism genome-scale metabolic network
RefDbcache | Reference data for global metabolic construction The reference metabolic pathway data contains KOs, substrates and products, as well as a constructed reference global network, which used for metabolic network reconstruction
RevEcoR | The RevEcoR package
seedset-class | 'seedset-class'
seedSize | Size of the each seed source component
seedSize-method | Size of the each seed source component
seedSize-methods | Size of the each seed source component
show | The show generic function
show-method | The show generic function
show-methods | The show generic function