RevEcoR: Reverse Ecology Analysis on Microbiome
Version 0.99.3

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.

AuthorYang Cao, Fei Li
Date of publication2016-04-03 17:14:01
MaintainerYang Cao <yiluheihei@gmail.com>
LicenseGPL (>= 2)
Version0.99.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RevEcoR")

Getting started

README.md
Revse Ecology Analysis on Microbiome"

Popular man pages

anno.species: Annotation profiles of seven well-studied oral species
calculateCooperationIndex: Calculating the metabolic competition and complementarity...
getOrgMetabolicData: Get organism metabolic data from KEGG database
getSeedSets: Identify seed compounds of each organism
Interactions: Calculating the species interactions
kegg_buc: Metabolic profiles of KEGG organism Buchnera aphidicola APS...
RevEcoR: The RevEcoR package
See all...

All man pages Function index File listing

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

Functions

Interactions Man page
KosarajuSCC Man page Source code
RefDbcache Man page
RevEcoR Man page
RevEcoR-package Man page
\%.\% Man page
anno.species Man page
calculateCooperationIndex Man page Source code
check.seedset Source code
competitionIndex Man page Source code
complementarityIndex Man page Source code
compose Man page Source code
confidencescore Man page
confidencescore,seedset-method Man page
confidencescore-methods Man page
getGsMN Man page
getGsMN,seedset-method Man page
getGsMN-methods Man page
getOrgMetabolicData Man page Source code
getSeedSets Man page Source code
gut_microbiome Man page
kegg_buc Man page
kegg_ptr Man page
len Man page
len,seedset-method Man page
len-methods Man page
nonseed Man page
nonseed,seedset-method Man page
nonseed-methods Man page
reconstructGsMN Man page Source code
seedSize Man page
seedSize,seedset-method Man page
seedSize-methods Man page
seedset-class Man page
show Man page
show,seedset-method Man page
show-methods Man page

Files

inst
inst/extdata
inst/extdata/koanno.tab
inst/extdata/occurrence.tab
inst/doc
inst/doc/RevEcoR.Rmd
inst/doc/RevEcoR.R
inst/doc/RevEcoR.html
NAMESPACE
data
data/anno.species.rda
data/RefDbcache.rda
data/kegg_buc.rda
data/kegg_ptr.rda
data/gut_microbiome.rda
R
R/AllClasses.R
R/RevEcoR.R
R/calculateCooperationIndex.R
R/gut_microbiome.R
R/kegg_buc.R
R/RefDbcache.R
R/reconsructGsMN.R
R/getOrgMetabolicData.R
R/KosarajuSCC.R
R/anno.species.R
R/compose.R
R/kegg_ptr.R
R/getSeedSets.R
vignettes
vignettes/RevEcoR.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/calculateCooperationIndex.Rd
man/Interactions.Rd
man/KosarajuSCC.Rd
man/compose.Rd
man/RevEcoR.Rd
man/getSeedSets.Rd
man/kegg_buc.Rd
man/len-methods.Rd
man/kegg_ptr.Rd
man/gut_microbiome.Rd
man/getOrgMetabolicData.Rd
man/seedset-class.Rd
man/seedSize-methods.Rd
man/nonseed-methods.Rd
man/confidencescore-methods.Rd
man/anno.species.Rd
man/RefDbcache.Rd
man/reconstructGsMN.Rd
man/getGsMN-methods.Rd
man/show-methods.Rd
RevEcoR documentation built on May 20, 2017, 1:56 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.