This repository contains code used for the analyses in the manuscript "IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies" by Friedrich, Pohin, and Jackson et al., Nature Medicine, 2021. It is divided into folders, each concerning a different data type or analytical approach. These are briefly outlined below.
This contains the WGCNA analyses used to define the modules in the discovery resection dataset, any analyses done using the modules in the discovery whole tissue RNA-Seq data, and the module replications in the therapy response datasets.
Added by Matthew Jackson
This contains notebooks used to perform quality control, exploratory analysis, and differential expression in the discovery resection and discovery whole tissue RNA-Seq datasets.
Added by Kevin Rue-Albrecht
This contains notebooks used to perform quality control, exploratory analysis, and differential expression in culture-expanded primary stromal cell lines from surgically resected intestinal tissue of IBD patients and stimulated them with a panel of cytokines.
Added by Kevin Rue-Albrecht
This contains notebooks used to perform quality control, exploratory analysis, and differential expression in FACS-sorted hematopoietic and non-hematopoietic cell subsets from the intestinal tissue of non-IBD and IBD patients.
Added by Kevin Rue-Albrecht
This contains all code associated with the analysis of single-cell data.
Added by Ilya Korsunsky