Jennifer Klunk*, Tauras P. Vilgalys*, Christian E. Demeure, Mari Shiratori, Julien Madej, Rémi Beau, Derek Elli5, Rebecca Redfern, Sharon N. DeWitte, Julia Gamble, Jesper L. Boldsen, Ann Carmichael, Nükhet Varlik, Katherine Eaton, Jean-Christophe Grenier, G. Brian Golding, Alison Devault, Jean-Marie Rouillard, Vania Yotova, Renata Sindeaux, Anne Dumaine, Jessica F Brinkworth, Dominique Missiakas, Guy A. Rouleau, Javier Pizarro-Cerdá, Hendrik N. Poinar^, Luis Barreiro^

*These authors contributed equally to this work, and are presented in alphabetical order ^These authors jointly supervised this work

We've divided the code and analyses in this repository to four sections based on the major data types used in these analyses. For convenience, we include processed data and results files which can be used to recreate the figures in our manuscript.

1. ancient genomes: identifying candidate variants for positive selection during the black death using ancient genomes and estimate the strength of selection at these variants

2. expression in macrophages: monocyte-derived macrophage gene expression in response to Yersinia pestis stimulation

3. expression in PBMCs: gene expression in peripheral blood mononucleocytes simulated with Y. pestis

4. cytokine data: cytokine levels in macrophages responding to Y. pestis stimulation

If you have any questions regarding the code in this repository, please contact Tauras Vilgalys (taur.vil at gmail.com).