covid_balf

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)

seurat_integration.R

Integration of all samples with seurat.

macrophage_integration.R

Integration of macrophage data with seurat.

NKT_integration.R

Integration of NK&T data with seurat.

T_integration.R

Integration of T data with seurat.

total_fig.R

code to generate all sample figures.

macrophage_fig.R

code to generate macrophage related figures.

NKT.R

code to generate NK&T related figures.

cytokine_fig.R

code to generate cytokine related figures.

tcr_fig.R

code to generate TCR related figures.

meta.txt

Meta data for samples.

all.cell.annotation.meta.txt

Cell type annotations for total cells.

myeloid.cell.annotation.meta.txt

Cell type annotations for macrophages.

NKT.cell.annotation.meta.txt

Cell type annotations for NK&T cells.

nCov.rds

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.