Hi all,

After running as instruction message I still got error:

    pip install --user scikit-misc

    sc.pp.highly_variable_genes(adata, n_top_genes = 2000, subset = True, flavor = 'seurat_v3')

ModuleNotFoundError                       Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/scanpy/preprocessing/_highly_variable_genes.py in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, inplace)
     52     try:
---> 53         from skmisc.loess import loess
     54     except ImportError:

ModuleNotFoundError: No module named 'skmisc'

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
2 frames
/usr/local/lib/python3.7/dist-packages/scanpy/preprocessing/_highly_variable_genes.py in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, inplace)
     54     except ImportError:
     55         raise ImportError(
---> 56             'Please install skmisc package via `pip install --user scikit-misc'
     57         )
     58     df = pd.DataFrame(index=adata.var_names)

ImportError: Please install skmisc package via `pip install --user scikit-misc

---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------

The code is from: https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb

Thank you so much!