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 |