/AnnotatedPBMC

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AnnotatedPBMC

Provides processed single-cell gene expression and cell type annotations for published peripheral blood mononuclear cell (PBMC) datasets as Bioconductor SingleCellExperiment objects.

The interface is simple: functions are in the form get_DATASET(cache_path) where DATASET is one of either

  • 10x_pbmc_10k
  • 10x_pbmc_5k_v3
  • 10x_sorted
  • blish_2020
  • ding_2019
  • haniffa_2021
  • hao_2020
  • kotliarov_2020
  • su_2020
  • tsang_2021

and cache_path is a user-specified file path.

Interested users are encouraged to look at the source code for processing details.

References and original download links are included in the function documentation. Cells are filtered to have at least 200 genes expressed and less than 10% mitochondrial reads, and are log-normalized.