Christina Theodoris commited on
Commit
d468697
1 Parent(s): e606e1c

Update instructions in tokenizing example to clarify requirement for Ensembl ID

Browse files
examples/tokenizing_scRNAseq_data.ipynb CHANGED
@@ -15,7 +15,9 @@
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  "id": "350e6252-b783-494b-9767-f087eb868a15",
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  "metadata": {},
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  "source": [
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- "#### Input data is a directory with .loom files containing raw counts from single cell RNAseq data, including all genes detected in the transcriptome without feature selection. Genes should be labeled with Ensembl IDs, which provide a unique identifer for conversion to tokens.\n",
 
 
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  "\n",
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  "#### No cell metadata is required, but custom cell attributes may be passed onto the tokenized dataset by providing a dictionary of custom attributes to be added, which is formatted as loom_col_attr_name : desired_dataset_col_attr_name. For example, if the original .loom dataset has column attributes \"cell_type\" and \"organ_major\" and one would like to retain these attributes as labels in the tokenized dataset with the new names \"cell_type\" and \"organ\", respectively, the following custom attribute dictionary should be provided: {\"cell_type\": \"cell_type\", \"organ_major\": \"organ\"}. \n",
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  "\n",
 
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  "id": "350e6252-b783-494b-9767-f087eb868a15",
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  "metadata": {},
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  "source": [
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+ "#### Input data is a directory with .loom files containing raw counts from single cell RNAseq data, including all genes detected in the transcriptome without feature selection. \n",
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+ "\n",
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+ "#### Genes should be labeled with Ensembl IDs (row attribute \"ensembl_id\"), which provide a unique identifer for conversion to tokens.\n",
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  "\n",
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  "#### No cell metadata is required, but custom cell attributes may be passed onto the tokenized dataset by providing a dictionary of custom attributes to be added, which is formatted as loom_col_attr_name : desired_dataset_col_attr_name. For example, if the original .loom dataset has column attributes \"cell_type\" and \"organ_major\" and one would like to retain these attributes as labels in the tokenized dataset with the new names \"cell_type\" and \"organ\", respectively, the following custom attribute dictionary should be provided: {\"cell_type\": \"cell_type\", \"organ_major\": \"organ\"}. \n",
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  "\n",