Code for community-wide metabolic modelling, calculation of metabolite exchange scores (MES) and statistical tests
Authors/Creators
- 1. Hudson Institute of Medical Research
- 2. Institute for Systems Biology
- 3. Monash University
Description
This repository contains the Python and R scripts needed to reproduce the analyses and graphs of the manuscript "Disease-specific loss of microbial cross-feeding interactions in the human gut".
Additionally, this repository contains the Metagenome Assembled Genomes (MAGs) reconstructed. You can find here:
* 24,369 high-quality MAGs (>90% completeness and <0.05% contamination). (all_HQ_bins_fasta.tar.gz)
* 955 species-level MAGs (i.e. clustered at 95% ANI), used to build genome-scale metabolic models (nucleotide and aminoacid - spp_level_representative_MAGs.zip).
This repository also contains the metabolic exchanges obtained from the community-wide modelling analysis (MICOM).
Version 1.2.1 - updated README + added scripts to produce new figures + removed obsolete code
Files
2_exchanges.zip
Files
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