CortexDataset

class scvi.dataset.CortexDataset(save_path='data/', genes_to_keep=None, total_genes=558, delayed_populating=False)

Bases: scvi.dataset.dataset.DownloadableDataset

Loads cortex dataset.

The Mouse Cortex Cells dataset contains 3005 mouse cortex cells and gold-standard labels for seven distinct cell types. Each cell type corresponds to a cluster to recover. We retain top 558 genes ordered by variance.

Parameters

• save_path (strstr) – Path indicating where to save/load data.

• genes_to_keep (List[str], NoneOptional[List[str]]) – Gene names to keep.

• total_genes (int, NoneOptional[int]) – Total number of genes to keep. If None and genes_to_keep is empty/None, all genes are loaded.

• delayed_populating (boolbool) – Boolean switch for delayed population mechanism.

Examples

>>> gene_dataset = CortexDataset()

Methods Summary

populate()

Populates a DonwloadableDataset object’s data attributes.

Methods Documentation

populate()

Populates a DonwloadableDataset object’s data attributes.

E.g by calling one of GeneExpressionDataset’s populate_from... methods.