Extract cell name from scvi dataset

Help
1

Dear scverse team,

I’ve loaded dataset using CsvDataset command, and because it goes through downsampling, I would like to extract cell names of the processed datasets - but was having difficulty finding the script for it. How would I extract the cell names of the loaded dataset (example below)?

GeneExpressionDataset object with n_cells x nb_genes = 32791 x 550
gene_attribute_names: ‘gene_names’
cell_attribute_names: ‘local_means’, ‘labels’, ‘local_vars’, ‘batch_indices’
cell_categorical_attribute_names: ‘labels’, ‘batch_indices’

Thank you,

Best regards,
Chloe

2

Hi Chloe,

It seems you are using an extremely old version of scvi. Can you try using scvi-tools?

3

Hi Adam,

Thank you for the reply. I was trying to run gimVI and all the examples were guiding towards scvi.dataset etc. Would there be a way to extract cell names from the existing data? or force not to do downsampling (of the cells) when loading the data?

Thank you,

Best regards,
Chloe