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mdine

Microbiome Differential Network Estimation (mdine) allows the estimation of OTU co-occurrence networks within two separate groups, where the networks are defined through precision matrices. The difference between the two precision matrices is also estimated, along with corresponding interval estimates. This work was developed in the Greenwood Lab at McGill University.

Installation

The first step to installing mdine is to install rstan along with the appropriate compiler. The steps on how to do this are different based on your OS:

Installing mdine for Mac/Linux

  • Install rstan by going to the installation page and following the Mac/Linux instructions.
    • Make sure you have a C++ toolchain and configuration installed as described in the instructions.

Once rstan has been successfully installed, run the following code to install mdine:

  • Run the following code in R:
if (!require(devtools)) {
  install.packages("devtools")
  library(devtools)
}
install_github("kevinmcgregor/mdine", dependencies=TRUE)

Installing mdine Windows

  • Install rstan by going to the installation page and following the Windows instructions.
    • Make sure to install rtools as described in the instructions.

Once rstan has been successfully installed, run the following code to install mdine:

  • Run the following code in R:
if (!require(devtools)) {
  install.packages("devtools")
  library(devtools)
}
install_github("kevinmcgregor/mdine", dependencies=TRUE)

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