This repository contains all code and results supporting the analysis of our manuscript titled 'Early prediction of preeclampsia using the first trimester vaginal microbiome.'
| Folder/file | Description |
|---|---|
code/ |
Contains code to run all analyses (reads from data/, writes to results/) |
code/immune-factor-associations |
analyses of immune factor associations (Fig. 2) |
code/microbe-associations |
analyses of microbe associations (Fig. 3) |
code/multiomic-associations |
analysis of immune factor associations (Fig. 4) |
code/predictions |
Contains code to run all prediciton analysies (Figs. 5,6) |
data/ |
Placeholder to directory containing all input data used to run analyses |
results/ |
Contains all figures images |
results/immune-factor-associations |
results of immune factor associations (Fig. 2) |
results/microbe-associations |
results of microbe associations (Fig. 3) |
results/multiomic-associations |
results of immune factor associations (Fig. 4) |
results/predictions |
results for all prediciton analysies (Figs. 5,6) |
preprocessing/ |
Contains commands used for preprocessing & quantification of metagenomic samples |
run.sh |
Script to run all analyses |
All analyses can be executed by executing the command bash run.sh from this repository's home directory. Running this script will populate all folders in the results directory with the files