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{
"cells": [
{
"cell_type": "markdown",
"id": "a91bca46-c056-4784-8c6c-b0f5d3f33496",
"metadata": {
"tags": []
},
"source": [
"## Tokenizing .loom single cell RNA-seq data to rank value encoding .dataset format"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "080fdd9c-0c48-4d5d-a254-52b6c53cdf78",
"metadata": {},
"outputs": [],
"source": [
"from geneformer import TranscriptomeTokenizer"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9641b146-af2c-4688-9d8a-9c570246d116",
"metadata": {},
"outputs": [],
"source": [
"tk = TranscriptomeTokenizer({\"cell_type\": \"cell_type\", \"organ_major\": \"organ_major\"}, nproc=4) # Dictionary of custom attributes to be added to the dataset.\n",
"tk.tokenize_data(\"loom_data_directory\", \"output_directory\", \"output_prefix\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
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"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
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"nbformat": 4,
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