Reverse Ecology Analysis on Microbiome

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.


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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Reference manual

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install.packages("RevEcoR")

0.99.3 by Yang Cao, 3 years ago


Browse source code at https://github.com/cran/RevEcoR


Authors: Yang Cao , Fei Li


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Matrix, igraph, XML, stringr, magrittr, gtools, plyr, purrr, methods

Suggests knitr


See at CRAN