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Reverse Ecology analysis in R

This package implements 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 the organism and their environment and the interactions among species.

Prerequisites

RevEcoR is free available on CRAN. You can install the latest released version from CRAN as following:

install.packages("RevEcoR") 

or the latest development version from github. To install packages from GitHub, you first need install the devtools package on your system with install.packages("devtools"). Note that devtools sometimes needs some extra non-R software on your system -- more specifically, an Rtools download for Windows or Xcode for OS X. There's more information about devtools here.

if (!require(devtools) 
  install.packages("devtools") 
devtools::install_github("yiluheihei/RevEcoR") 

After installation, you can load RevEcoR into current workspace by typing or pasting the following codes:

library("RevEcoR")

Contributing

For very simple changes such as fixing typos, you can just edit the file by clicking the button Edit. For more complicated changes, you will have to manually create a pull request after forking this repository.

##License

RevEcoR is a free and open source software, licensed under GPL 2.0.

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Version

Install

install.packages('RevEcoR')

Monthly Downloads

230

Version

0.99.3

License

GPL (>= 2)

Maintainer

Yang Cao

Last Published

April 3rd, 2016

Functions in RevEcoR (0.99.3)

KosarajuSCC

Caculating the strong connected components (SCC) of a 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
compose

Compose multiple functions
calculateCooperationIndex

Calculating the metabolic competition and complementarity index
RevEcoR

The RevEcoR package
len-methods

the length of the seed set
Interactions

Calculating the species interactions
getOrgMetabolicData

Get organism metabolic data from KEGG database
show,seedset-method

The show generic function
kegg_buc

Metabolic profiles of KEGG organism Buchnera aphidicola APS (Acyrthosiphon pisum) (KEGG organism code: buc)
anno.species

Annotation profiles of seven well-studied oral species
getGsMN-methods

The genome scale metabolic network
kegg_ptr

Metabolic profiles of KEGG organism Pan troglodytes (chimpanzee) (KEGG organism code: ptr)
nonseed-methods

Non seed of the network
gut_microbiome

Annotation profiles of 116 gut prevalent species
getSeedSets

Identify seed compounds of each organism
seedset-class

seedset-class
seedSize-methods

Size of the each seed source component
reconstructGsMN

Reconstuction of the specific-organism genome-scale metabolic network
confidencescore-methods

Conficence score