Analyses pertaining to the manuscruipt Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome
William F. Kindschuh1*, Federico Baldini1*, Martin C. Liu1,2*, Jingqiu Liao1, Yoli Meydan1, Harry H.Lee1, Almut Heinken3, Ines Thiele3,4,5,6, Maayan Levy7&, Tal Korem1,8,9&
Author affiliations:
1 Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY
2 Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY
3 School of Medicine, National University of Ireland, Galway, Galway, Ireland
4 Discipline of Microbiology, National University of Galway, Galway, Ireland
5 Ryan Institute, National University of Galway, Galway, Ireland
6 APC Microbiome Ireland, University College Cork, Cork, Ireland
7 Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
8 Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
9 CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
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- these authors contributed equally to this work
& - corresponding authors, Tal Korem (tk2829@cumc.columbia.edu) and Maayan Levy (maayanle@pennmedicine.upenn.edu)
To install required dependencies run the following command: "conda env create -f ptb_metabs.yml"
To reproduce the analyses and panels run the following commands: "python generate_figures.py" "python generate_prediction_figures.py"
Note - in order to avoid having to regenerate the null distributions of p-values required for the msea (extended data figure 5d) you will need to unzip the zipped p-value files contained within data/msea