RevEcoR: Reverse Ecology Analysis on Microbiome

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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.

Author
Yang Cao, Fei Li
Date of publication
2016-04-03 17:14:01
Maintainer
Yang Cao <yiluheihei@gmail.com>
License
GPL (>= 2)
Version
0.99.3

View on CRAN

Man pages

anno.species
Annotation profiles of seven well-studied oral species
calculateCooperationIndex
Calculating the metabolic competition and complementarity...
compose
Compose multiple functions
confidencescore-methods
Conficence score
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...
kegg_ptr
Metabolic profiles of KEGG organism Pan troglodytes...
KosarajuSCC
Caculating the strong connected components (SCC) of a network
len-methods
the length of the seed set
nonseed-methods
Non seed of the network
reconstructGsMN
Reconstuction of the specific-organism genome-scale metabolic...
RefDbcache
Reference data for global metabolic construction The...
RevEcoR
The RevEcoR package
seedset-class
'seedset-class'
seedSize-methods
Size of the each seed source component
show-methods
The show generic function

Files in this package

RevEcoR
RevEcoR/inst
RevEcoR/inst/extdata
RevEcoR/inst/extdata/koanno.tab
RevEcoR/inst/extdata/occurrence.tab
RevEcoR/inst/doc
RevEcoR/inst/doc/RevEcoR.Rmd
RevEcoR/inst/doc/RevEcoR.R
RevEcoR/inst/doc/RevEcoR.html
RevEcoR/NAMESPACE
RevEcoR/data
RevEcoR/data/anno.species.rda
RevEcoR/data/RefDbcache.rda
RevEcoR/data/kegg_buc.rda
RevEcoR/data/kegg_ptr.rda
RevEcoR/data/gut_microbiome.rda
RevEcoR/R
RevEcoR/R/AllClasses.R
RevEcoR/R/RevEcoR.R
RevEcoR/R/calculateCooperationIndex.R
RevEcoR/R/gut_microbiome.R
RevEcoR/R/kegg_buc.R
RevEcoR/R/RefDbcache.R
RevEcoR/R/reconsructGsMN.R
RevEcoR/R/getOrgMetabolicData.R
RevEcoR/R/KosarajuSCC.R
RevEcoR/R/anno.species.R
RevEcoR/R/compose.R
RevEcoR/R/kegg_ptr.R
RevEcoR/R/getSeedSets.R
RevEcoR/vignettes
RevEcoR/vignettes/RevEcoR.Rmd
RevEcoR/README.md
RevEcoR/MD5
RevEcoR/build
RevEcoR/build/vignette.rds
RevEcoR/DESCRIPTION
RevEcoR/man
RevEcoR/man/calculateCooperationIndex.Rd
RevEcoR/man/Interactions.Rd
RevEcoR/man/KosarajuSCC.Rd
RevEcoR/man/compose.Rd
RevEcoR/man/RevEcoR.Rd
RevEcoR/man/getSeedSets.Rd
RevEcoR/man/kegg_buc.Rd
RevEcoR/man/len-methods.Rd
RevEcoR/man/kegg_ptr.Rd
RevEcoR/man/gut_microbiome.Rd
RevEcoR/man/getOrgMetabolicData.Rd
RevEcoR/man/seedset-class.Rd
RevEcoR/man/seedSize-methods.Rd
RevEcoR/man/nonseed-methods.Rd
RevEcoR/man/confidencescore-methods.Rd
RevEcoR/man/anno.species.Rd
RevEcoR/man/RefDbcache.Rd
RevEcoR/man/reconstructGsMN.Rd
RevEcoR/man/getGsMN-methods.Rd
RevEcoR/man/show-methods.Rd