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/ <strong>References:</strong> [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

适配cell2cell工具的数据集可从以下地址获取：https://github.com/earmingol/cell2cell。本版本包含一项支气管肺泡灌洗液（Bronchoalveolar Lavage Fluid, BALF）新冠数据集，该数据集涵盖3名健康对照者、3名中度新冠患者及6名重度新冠患者肺部组织中的63000个免疫细胞与上皮细胞。该数据集此前已发表于文献[1]，本数据集对象包含注释细胞类型的原始基因计数数据，完整的注释细胞类型原始计数数据可从以下地址获取：https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145926。本次我们以h5ad格式与Seurat对象的形式提供该原始基因计数数据。此外，基因通路注释文件（.gmt格式）获取自：https://www.gsea-msigdb.org/。<strong>参考文献：</strong> [1] Liao M, Liu Y, Yuan J, et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19[J]. Nature Medicine, 2020, 26: 842-844. https://doi.org/10.1038/s41591-020-0901-9