Reverse Ecology Analysis on Microbiome

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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