A modified Mediterranean ketogenic diet mitigates modifiable risk factors of Alzheimer’s disease: a serum and CSF-based metabolic analysis
This repository contains scripts for analysis and figure generation of the paper
Schweickart*, Batra* et. al. A modified Mediterranean ketogenic diet mitigates modifiable risk factors of Alzheimer’s disease: a serum and CSF-based metabolic analysis (2023), medRxiv. link
Script name | Description |
---|---|
custom_functions.R | Internal customized functions. Will be sourced by other scripts |
1_serum_dataprocessing.R | BEAM serum metabolomics preprocessing |
2_serum_association_analysis.R | BEAM serum association analysis |
3_csf_dataprocessing.R | BEAM CSF metabolomics preprocessing |
4_csf_association_analysis.R | BEAM CSF association analysis |
5_metabolome_figures.R | Figures 2a, 2b, 2d, 3a, 4 (Figures 1, 3b, and 4 (partially) were manually generated) |
6a_joint-tensor-nightingale-microbiome.ipynb | Microbiome analysis |
6b_joint_tensor_factorization_microbiome_nightingale.R | Microbiome-metabolme joint analysis |
6c_microbiome_figures.R | Figure 2c |
Folder | Description |
input | Contains the input data to be used by the scripts |
results | Will contain output files |
Output files in results/ | Description |
tmp* | Intermediate files used in follow-up scripts |
supplementary* | Supplementary files from the paper |
Figure* | Figure panels from the paper |
Input files for scripts: tmp_annotations_sig_serum_diet.csv is provided with content in the input folder.
Run scripts in sequence 1 to 5 for metabolomics analysis and figures. Run scripts 6a, 6b, 6c for microbiome analysis and figures.