Skip to contents

COVID-19 PBMC Query (Severe COVID-19) Single-Cell RNA-Seq Dataset

Source: R/dataDocumentation.R
covid_query_data.Rd

This dataset contains a downsampled query (severe COVID-19 donor) subset of the Stephenson et al. (2021) COVID-19 PBMC atlas, for use alongside covid_reference_data. Cell types are annotated using Azimuth reference mapping (azimuth_celltype_l1_merged).

Usage

covid_query_data

Format

An object of class SingleCellExperiment with 414 rows and 1330 columns.

Source

Stephenson E, et al. (2021), processed and hosted at https://doi.org/10.5281/zenodo.18274942.

Details

See covid_reference_data for the shared processing steps. CD14 monocytes, the focus of the accompanying case study vignette, are downsampled to at most 450 cells (other cell types to at most 220) so the interferon-activated subset described in the manuscript stays well-represented.

References

Stephenson E, et al. (2021). Single-cell multi-omics analysis of the immune response in COVID-19. Nature Medicine 27:904-916.

See also

Use data("covid_query_data") to load and access the resulting query dataset, and data("covid_reference_data") for comparison with the reference dataset.

Examples

# Load and explore the COVID-19 query dataset
data("covid_query_data")