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update headers and paths
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tony-kuo committed Feb 13, 2024
1 parent b72037c commit 3b38264
Showing 1 changed file with 4 additions and 6 deletions.
10 changes: 4 additions & 6 deletions docs/notebooks/cell_search_tutorial_1.ipynb
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"source": [
"# Instantiate the CellQuery object.\n",
"# Replace model_path with your local file path.\n",
"from scimilarity import ModelPath\n",
"model_path = ModelPath.model_paper\n",
"model_path = '/models/model_v1'\n",
"cq = CellQuery(model_path)"
]
},
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"id": "3b5ba1f3-4371-4b1f-9165-8d84f5377c96",
"metadata": {},
"source": [
"### Compute visualization of embeddings\n",
"#### Use UMAP to visualize SCimilarity embeddings"
"### Compute visualization of embeddings"
]
},
{
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"id": "a3aac50b-09c3-4d2d-b66e-208d476773cd",
"metadata": {},
"source": [
"**GSM4058950** contains good quality myofibroblasts (based on the expression of myofibroblast canonical markers) "
"GSM4058950 contains good quality myofibroblasts (based on the expression of myofibroblast canonical markers) "
]
},
{
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"id": "3cfde83f-e498-424e-9d55-fdbf2b872aec",
"metadata": {},
"source": [
"##### Exclude self-referencing results\n",
"#### Exclude self-referencing results\n",
"Naturally, queries searching for similar cells will highlight cells from the same study. To get a clearer view of the results, we often exclude those self-referencing hits."
]
},
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