Nutrition_microbiome_reproducibility: reproduction of the figures of "Sugar-rich foods exacerbate antibiotic-induced microbiome disruption"
Authors/Creators
- 1. Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Contributors
Researcher (4):
- 1. Institute for Systems Genetics and Department of Microbiology, NYU Langone Health Grossman School of Medicine, New York, NY, USA
- 2. Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- 3. Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Description
This repository facilitates reproduction of the figures from the manuscript "Sugar-rich foods exacerbate antibiotic-induced microbiome disruption", built from a small set of de-identified released tables. Every panel is rebuilt by a numbered R script that reads only from released_data/ and writes one PDF per panel.
Scripts are organised by analysis family rather than by printed figure: expensive Bayesian models are fit once and cached, then consumed by the panels that need them. The inputs needed for figure generation are available, including de-identified patient-level clinical-outcome and medication tables.
The accompanying article is published in Nature: https://doi.org/10.1038/s41586-026-11077-3. Please cite the article in preference to this software.
Files
Anqi-Dai/Nutrition_microbiome_reproducibility-v1.3.0.zip
Additional details
Related works
- Is supplement to
- Journal article: 10.1038/s41586-026-11077-3 (DOI)
- References
- Dataset: 10.5281/zenodo.14538105 (DOI)