Extended duration of gut microbiota depletion reverses protection from experimental autoimmune uveitis

This repository contains scripts/code used for analyzing the microbiome and nanostring data in this study.

• Authors: Vijay Nagarajan PhD
• Affiliation: Laboratory of Immunology, NEI/NIH
• Contact: [email protected]
• Platform: The workflow BASH commands were developed to run on a Mac OS, but could be reused/reproduced in any unix environment with appropriate changes
• Publication: Salvador R, Horai R, Zhang A, Jittayasothorn Y, Tang J, Gupta A, Nagarajan V, Caspi RR. Too Much of a Good Thing: Extended Duration of Gut Microbiota Depletion Reverses Protection From Experimental Autoimmune Uveitis. Invest Ophthalmol Vis Sci. 2023 Nov 1;64(14):43. doi: 10.1167/iovs.64.14.43. PMID: 38019490; PMCID: PMC10691388.

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1. Tools/nsolver_extract.sh This bash script takes nanostring/nsolver DE file and extracts filtered DGE lists, filtered DGE names, ids, cleans ids, writes file for geo matrix and cytoscape input
2. Tools/tabtogmt.R This R script reads in a tab delimited gene set file and generates the gmt format input file for gsea.
3. Tools/gseaonly.sh This bash script reads in the gsea input, gmt file and generates gsea output for all samples in a folder
4. Tools/enrichmentPlotsGsea.R This R script reads lists of GSEA generated enrichment TSV files and generates a plot with all the results in one panel.