Download the Kang, et al. IFN-beta stimulated PBMC data

Downloads the Kang, et al. demultiplexed PBMC experiment as a SingleCellExperiment. 8 lupus donors, PBMCs, control against IFN-beta stimulated in vitro, roughly 29k cells before quality control.

The design is paired within donor, which is what makes it the example for nebula_sc(): the donor is a genuine random effect and every donor contributes to both arms. Load it with load_sce().

Usage

download_kang_pbmc(quiet = FALSE)

Arguments

quiet

Boolean. If the download shall be quiet.

Value

String. The path to the qs2 file holding the SingleCellExperiment.

Details

Sourced from the muscData Bioconductor package, itself from GEO accession GSE96583. See data-raw/zenodo_sce_datasets.R for the preparation. The multiplets column marks doublets and ambiguous droplets, which are worth dropping before any modelling.

Served from the bixverse-data GitHub release. There is no Zenodo fallback for this one yet.

References

Kang, et al., Nat. Biotechnol., 2018

Examples

if (FALSE) { # \dontrun{
# pulls the archive into the session tempdir()
path <- download_kang_pbmc()
sce <- qs2::qs_read(path)
} # }