Source_code_for_SCFA_dynamics_project

Computational analysis of gut microbiome and SCFA (acetate, butyrate, propionate) time series data

Folder (need to be cleaned)

our_data: original and processed data generated by this project literature_data: published data in the literature (human gut microbiota responses under inulin intervention) codes: each folder correspondes to one main text figure and its associated supplementary figures figures: AI-editable figures created for the manuscript references: relevant papers

To run the codes, the following third-party packages/databases are required

1. Cmdstan (https://mc-stan.org/users/interfaces/cmdstan) for inulin responder detection in Fig.4
2. seqNMF (https://github.com/ContextLab/seqnmf) for factor analysis in Fig.3