Subspecies phylogeny in the human gut revealed by coevolutionary constraints across the bacterial kingdom

Initializing project

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

Doran_etal_2023

This project reproduces results from:

Subspecies phylogeny in the human gut revealed by coevolutionary constraints across the bacterial kingdom

To (locally) reproduce this project, do the following:

0. Download this code base.

   git clone --recurse-submodules git@github.com:aramanlab/Doran_etal_2023.git
   cd Doran_etal_2023

1. Open a Julia console and do:

   julia> # press ']' to enter package mode
   (1.10) pkg> add DrWatson # install globally, for using `quickactivate`
   (1.10) pkg> activate "path/to/this/project"
   (Doran_etal_2023) pkg> instantiate

This will install all necessary packages for you to be able to run the scripts and everything should work out of the box, including correctly finding local paths.

You may notice that most scripts start with the commands:

using DrWatson
@quickactivate projectdir()

which auto-activates the project and enables local path handling from DrWatson.

SpectralInference.jl

This project uses our lab’s custom package SpectralInference.jl

To use the package for your own projects, please look at its separate github project.

https://github.com/aramanlab/SpectralInference.jl