All functions

Annotation profiles of seven well-studied oral species

• anno.species

Calculating the metabolic competition and complementarity index

• calculateCooperationIndex

Compose multiple functions

• %.%
• compose

Conficence score

• confidencescore
• confidencescore,seedset-method
• confidencescore-methods

The genome scale metabolic network

• getGsMN
• getGsMN,seedset-method
• getGsMN-methods

Get organism metabolic data from KEGG database

• getOrgMetabolicData

Identify seed compounds of each organism

• getSeedSets

Annotation profiles of 116 gut prevalent species

• gut_microbiome

Calculating the species interactions

• Interactions
• competitionIndex
• complementarityIndex

Metabolic profiles of KEGG organism Buchnera aphidicola APS (Acyrthosiphon

• kegg_buc

Metabolic profiles of KEGG organism Pan troglodytes (chimpanzee) (KEGG

• kegg_ptr

Caculating the strong connected components (SCC) of a network

• KosarajuSCC

the length of the seed set

• len
• len,seedset-method
• len-methods

Non seed of the network

• nonseed
• nonseed,seedset-method
• nonseed-methods

Reconstuction of the specific-organism genome-scale metabolic network

• reconstructGsMN

Reference data for global metabolic construction

• RefDbcache

The RevEcoR package

• RevEcoR
• RevEcoR-package

seedset-class

• seedset-class

Size of the each seed source component

• seedSize
• seedSize,seedset-method
• seedSize-methods

The show generic function

• show
• show,seedset-method
• show-methods