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notebook updates
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mbabadi committed Oct 7, 2024
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10 changes: 5 additions & 5 deletions notebooks/quickstart_tutorial.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"The response will contain a list of annotation models and their brief descriptions. You need to choose the model that is suitable for your dataset. For this tutorial, choose a model that is suitable for annotating human scRNA-seq datasets. At the time of writing, the default model is `cellarium-pca-default-v1`:"
"The response will contain a list of annotation models and their brief descriptions. You need to choose the model that is suitable for your dataset. For this tutorial, we set `cas_model_name` to `None`, which implies choosing the default model. The default model is suitable for annotating human scRNA-seq datasets."
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"# Select the annotation model\n",
"cas_model_name = 'cellarium-pca-default-v1'"
"# Select the annotation model; 'None' for choosing the default model\n",
"cas_model_name = None"
]
},
{
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" adata=adata, # the AnnData file\n",
" root_node=\"CL_0000255\", # set to CL root node to \"eukaryotic cell\"\n",
" cluster_label_obs_column=\"cluster_label\", # (optional) The .obs column name containing cluster labels \n",
" ).run(port=DASH_SERVER_PORT, debug=False, jupyter_width=\"1000\")"
" ).run(port=DASH_SERVER_PORT, debug=False, jupyter_width=\"100%\")"
]
},
{
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