Chunk #60 — Methods — Analysis of publicly available datasets — Single-cell RNA-seq data of bronchoalveolar immune cells in patients with COVID-19

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

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We used the annotated single-cell RNA-seq data of the bronchoalveolar lavage fluid cells from three patients with moderate COVID-19 progression, six patients with severe COVID-19 progression, four healthy donors, and a publicly available sample4. The cell-type annotations of all samples were provided at https://github.com/zhangzlab/covid_balf.