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fix: tiny preprocessing bug in complete sc analysis #13

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fix: tiny preprocessing bug in complete sc analysis #13

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2 changes: 1 addition & 1 deletion single_cell_analysis_complete_class.ipynb
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Expand Up @@ -3130,7 +3130,7 @@
" \n",
" sc.pp.filter_cells(adata, min_genes=200) #get rid of cells with fewer than 200 genes\n",
" #sc.pp.filter_genes(adata, min_cells=3) #get rid of genes that are found in fewer than 3 cells\n",
" adata.var['mt'] = adata.var_names.str.startswith('mt-') # annotate the group of mitochondrial genes as 'mt'\n",
" adata.var['mt'] = adata.var_names.str.startswith('MT-') # annotate the group of mitochondrial genes as 'mt'\n",
" adata.var['ribo'] = adata.var_names.isin(ribo_genes[0].values)\n",
" sc.pp.calculate_qc_metrics(adata, qc_vars=['mt', 'ribo'], percent_top=None, log1p=False, inplace=True)\n",
" upper_lim = np.quantile(adata.obs.n_genes_by_counts.values, .98)\n",
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