When I do this, it doesn't seem to download SCT assay. Does that mean it's not there yet? Same as rank assay.
conn, table = get_metadata(parquet_url = SAMPLE_DATABASE_URL)
table = table.filter("""
empty_droplet = 'false'
AND alive = 'true'
AND "scDblFinder.class" != 'doublet'
""")
query = table.filter("cell_type_unified_ensemble LIKE '%cd14%'")
adata_sct = get_single_cell_experiment(query, assays="sct")
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/shen.m/git_control/homebrew/lib/python3.11/site-packages/cellnexuspy/__init__.py", line 227, in get_single_cell_experiment
return _get_anndata(data, assays=assays, cell_aggregation="single_cell", cache_directory=_get_default_cache_dir(), features=features)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/shen.m/git_control/homebrew/lib/python3.11/site-packages/cellnexuspy/__init__.py", line 173, in _get_anndata
assert assays in (set(assay_map.keys()))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError
Hi,
When I do this, it doesn't seem to download SCT assay. Does that mean it's not there yet? Same as rank assay.
Cheers,
Mengyuan