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Gut Microbiome in Schizophrenia: Altered Functional Pathways Related to Immune Modulation and Atherosclerotic Risk

This repository includes code to replicate analyses presented in the Nguyen, Kosciolek et al. Brain, Behavior, and Immunity paper.

Nguyen TT, Kosciolek T, Daly RE, Vázquez-Baeza Y, Swafford A, Knight R, Jeste DV. Gut Microbiome in Schizophrenia: Altered Functional Pathways Related to Immune Modulation and Atherosclerotic Risk. Brain Behav Immun. 2020 Oct 21:S0889-1591(20)31682-2.  
doi: 10.1016/j.bbi.2020.10.003  
PMID: 33098964

data

EBI Accession: ERP107975
Qiita study: https://qiita.ucsd.edu/study/description/11710 ((prep ID 8769)

running notebooks

Before you start, please install the necessary software first:

Preferably, each in its own Conda environment.