lack processing data

[Ssupercoder]

I want to know where can I find “PBMC_merged.normal.subsample500cells.h5ad”，and I can not fint it in file named“20220531_PBMC_metadata.ipynb”.

[emdann]

Are you looking at the most recent version of this repo/analysis? Can you link to the specific notebook you are referring to?

[Ssupercoder]

Are you looking at the most recent version of this repo/analysis? Can you link to the specific notebook you are referring to?

We would like to use your data to reproduce the normal single-cell data preprocessing process, but in the path (src/1_PBMC_data_preprocessing/2_PBMC_scVI.ipynb , site: oor_design_reproducibility/src/1_PBMC_data_ preprocessing/2_PBMC_scVI.ipynb at master - MarioniLab/oor_design_reproducibility ) had missing data. We were unable to find data cleaned and filtered single cell data for training the scVI model.

[emdann]

You can find the data used for training the scVI model on figshare as PBMC_merged.normal.subsample500cells.clean_celltypes.h5ad

Here the count matrix is the same as used for scVI training, but the object additionally includes the embedding and clustering results (you can see how we went from PBMC_merged.normal.subsample500cells.h5ad to PBMC_merged.normal.subsample500cells.clean_celltypes.h5ad here).

[Ssupercoder]

Thank you！But I only want to use this data（PBMC_merged.normal.subsample500cells.h5ad）for training scVI model.In your package, Ican not find it