Performing seurat-style data integration on data analysed using scanpy?

[ivirshup]

I think this question is a bit different, since it’s not about accounting for batch effects in the data. I’ve addressed this in your other post here:

How to add additional metadata on multiple different single cell RNA files from different experiments, such as organ, sample number etc

Hey @Echoo-ranger, Could you add this information as columns of the obs dataframe before concatenation? If there is only one condition per cell ranger output, you could also add this information during concatenation with the label argument. Then the code should probably look something like: import scanpy as sc import anndata as ad # Read in each experiment experiment_dirs = ["organ1", "organ2", ...] experiment_adatas = { expr_name: sc.read_10x_h5(f"path/to/{expr_name}/outs/filtered_featur…