R script for the covid balf data analysis. (Liao M. et al, Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19, Nature Medicine, 2020. https://www.nature.com/articles/s41591-020-0901-9)

Integration of all samples with seurat.

Integration of macrophage data with seurat.

Integration of NK&T data with seurat.

Integration of T data with seurat.

code to generate all sample figures.

code to generate macrophage related figures.

code to generate NK&T related figures.

code to generate cytokine related figures.

code to generate TCR related figures.

Meta data for samples.

Cell type annotations for total cells.

Cell type annotations for macrophages.

Cell type annotations for NK&T cells.

The data has been deployed in https://covid19-balf.cells.ucsc.edu. And you can download the annotated Seurat rds file at http://cells.ucsc.edu/covid19-balf/nCoV.rds.