ERROR in pseudobulk_pyDeseq2.ipynb with pseudo replicates

[redvoidling]

Hi,

I was testing your tutorial on pseudobulk with pseudo replicates and I noticed that all the replicates created by your script are identical because you did not slice with the pseudo_rep slice that you created from the indices.

I propose you change this line:

from ` for i, pseudo_rep in enumerate(indices):

    rep_adata = sc.AnnData(X = samp_cell_subset.X.sum(axis = 0),
                           var = samp_cell_subset.var[[]])

`

to

rep_adata = sc.AnnData(X = samp_cell_subset[samp_cell_subset.obs_names.isin(pseudo_rep)].X.sum(axis = 0), var = samp_cell_subset.var[[]])

And thanks for the cool work you do :)