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RevEcoR (version 0.99.2)

Reverse Ecology Analysis on Microbiome

Description

An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.

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Version

Install

install.packages('RevEcoR')

Monthly Downloads

161

Version

0.99.2

License

GPL (>= 2)

Maintainer

Yang Cao

Last Published

June 8th, 2015

Functions in RevEcoR (0.99.2)

confidencescore-methods

Conficence score
compose

Compose multiple functions
RevEcoR

The RevEcoR package
gut_microbiome

Annotation profiles of 116 gut prevalent species
competitionIndex

Caculating the metabolic competition index
caculateCooperationIndex

Caculating the metabolic competition and complementarity index
KosarajuSCC

Caculating the strong connected components (SCC) of a network
complementarityIndex

Caculating the metabolic complementarity index
getSeedSets

Identify seed compounds of each organism
getGsMN-methods

The genome scale metabolic network
seedSize-methods

Size of the each seed source component
getOrgMetabolicData

Get organism metabolic data from KEGG database
len-methods

the length of the seed set
show,seedset-method

The show generic function
kegg_ptr

Metabolic profiles of KEGG organism Pan troglodytes (chimpanzee) (KEGG organism code: ptr)
anno.species

Annotation profiles of seven well-studied oral species
RefDbcache

Reference data for global metabolic construction
kegg_buc

Metabolic profiles of KEGG organism Buchnera aphidicola APS (Acyrthosiphon pisum) (KEGG organism code: buc)
seedset-class

seedset-class
nonseed-methods

Non seed of the network
reconstructGsMN

Reconstuction of the specific-organism genome-scale metabolic network