Christina Theodoris
commited on
Commit
·
f89f796
1
Parent(s):
ebe5ee8
Add example for tokenizing .loom dataset
Browse files
examples/tokenizing_scRNAseq_data.ipynb
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "a91bca46-c056-4784-8c6c-b0f5d3f33496",
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"metadata": {
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"tags": []
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},
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"source": [
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"## Tokenizing .loom single cell RNA-seq data to rank value encoding .dataset format"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "080fdd9c-0c48-4d5d-a254-52b6c53cdf78",
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"metadata": {},
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"outputs": [],
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"source": [
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"from geneformer import TranscriptomeTokenizer"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9641b146-af2c-4688-9d8a-9c570246d116",
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"metadata": {},
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"outputs": [],
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"source": [
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"tk = TranscriptomeTokenizer({\"cell_type\": \"cell_type\", \"organ_major\": \"organ_major\"}, nproc=4) # Dictionary of custom attributes to be added to the dataset.\n",
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"tk.tokenize_data(\"loom_data_directory\", \"output_directory\", \"output_prefix\")"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.11"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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