Datasets for cell2cell

Datasets for the tool cell2cell available in: https://github.com/earmingol/cell2cell

This version contains a BALF COVID-19 dataset that consists in 63k immune and epithelial cells in lungs from 3 control, 3 moderate COVID-19, and 6 severe COVID-19 patients.

This dataset was previously published in [1], and this object contains the raw counts for the annotated cell types available in: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145926

Here we make available the raw counts as h5ad and seurat objects.

Additionally, pathway annotations for genes (.gmt files) were obtained from: https://www.gsea-msigdb.org/

References:

[1] Liao, M., Liu, Y., Yuan, J. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat Med 26, 842–844 (2020). https://doi.org/10.1038/s41591-020-0901-9