Chunk #59 — Methods — Analysis of publicly available datasets — Single-cell RNA-seq data of ulcerative colitis in human donors

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scCODA is a Bayesian model for compositional single-cell data analysis.

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24 healthy, 21 non-inflamed, 16 inflamed) in Epi and data from 30 donors (72 samples, where 24 each healthy, non-inflamed, and inflamed, respectively) in LP. Specifically, we tested chain lengths of 20,000, 40,000, 80,000, and 150,000 iterations with a burn-in of 10,000 in the Epi case, while we tested chain lengths of 200,000, 400,000, and 800,000 iterations with a burn-in of 10,000 in the LP case due to the larger number of cell types in LP compared to Epi.