Data and code availability
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Data: Both raw and processed transcriptomic are available through the Gene Expression Omnibus (GEO: GSE180578). Additional data are available via Mendeley Data (Mendeley Data: http://doi.org/10.17632/r83csstphc.2).
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Code: The Seurat package was used for scRNaseq normalization, scaling, dimensionality reduction, UMAP visualization, clustering, and differential gene expression analysis. Code for these steps is available through Seurat’s website (https://satijalab.org/seurat/). Code for gene set enrichment analysis is available at https://www.github.com/arc85/singleseqgset. Code is provided at https://github.com/arc85/covid_analyses files to demonstrate gene module discovery, training of machine learning algorithms and leave one out cross validation analysis, and meta-analysis of infected myeloid cells.
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General statement: Any additional information required to reanalyze the data reported in this paper is available from the Lead Contact upon request.