Reverse Ecology Analysis on Microbiome


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Documentation for package ‘RevEcoR’ version 0.99.2

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RevEcoR-package The RevEcoR package
%.% Compose multiple functions
anno.species Annotation profiles of seven well-studied oral species
caculateCooperationIndex Caculating the metabolic competition and complementarity index
competitionIndex Caculating the metabolic competition index
complementarityIndex Caculating the metabolic complementarity index
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
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
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