PbmcDataset¶
-
class
scvi.dataset.PbmcDataset(save_path='data/', save_path_10X=None, remove_extracted_data=False, delayed_populating=False)[source]¶ Bases:
scvi.dataset.dataset.DownloadableDatasetLoads pbmc dataset.
We considered scRNA-seq data from two batches of peripheral blood mononuclear cells (PBMCs) from a healthy donor (4K PBMCs and 8K PBMCs). We derived quality control metrics using the cellrangerRkit R package (v. 1.1.0). Quality metrics were extracted from CellRanger throughout the molecule specific information file. After filtering, we extract 12,039 cells with 10,310 sampled genes and get biologically meaningful clusters with the software Seurat. We then filter genes that we could not match with the bulk data used for differential expression to be left with g = 3346.
- Parameters
save_path (
strstr) – Location to use when saving/loading the Pbmc metadata.save_path_10X (
str,NoneOptional[str]) – Location to use when saving/loading the underlying 10X datasets.remove_extracted_data (
boolbool) – Whether to remove extracted archives after populating the dataset.delayed_populating (
boolbool) – Switch for delayed populating mechanism.
Examples
>>> gene_dataset = PbmcDataset()
Methods Summary
populate()Populates a
DonwloadableDatasetobject’s data attributes.Methods Documentation