Skip to content

Supplementary data for co-occurrence manuscript

Notifications You must be signed in to change notification settings

cdanielmachado/cooccurrence

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

5 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Co-occurrence paper supplement

This repository contains all the data and code require to generate all the figures in the following paper:

Machado D. et al, Polarization of microbial communities in the competition-cooperation trade-off landscape (in preparation)

Usage

  • Please run download.sh to download and extract larger data files that cannot be hosted in github.

  • All the figures in the paper can be reproduced by running the respective jupyter notebook.

Tools

  • HiOrCo: computing higher-order co-occurrence species sets.

  • CarveMe: reconstruction of genome-scale metabolic models.

  • SMETANA: simulating cross-feeding interactions in microbial communities.