ctheodoris
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cb1b0d5
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Parent(s):
7470753
update instructions to include reminder about token dictionary
Browse files
examples/tokenizing_scRNAseq_data.ipynb
CHANGED
@@ -25,7 +25,11 @@
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"\n",
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"#### Additionally, if the original .loom file contains a cell column attribute called \"filter_pass\", this column will be used as a binary indicator of whether to include these cells in the tokenized data. All cells with \"1\" in this attribute will be tokenized, whereas the others will be excluded. One may use this column to indicate QC filtering or other criteria for selection for inclusion in the final tokenized dataset.\n",
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"\n",
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"#### If one's data is in other formats besides .loom or .h5ad, one can use the relevant tools (such as Anndata tools) to convert the file to a .loom or .h5ad format prior to running the transcriptome tokenizer
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{
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"\n",
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"#### Additionally, if the original .loom file contains a cell column attribute called \"filter_pass\", this column will be used as a binary indicator of whether to include these cells in the tokenized data. All cells with \"1\" in this attribute will be tokenized, whereas the others will be excluded. One may use this column to indicate QC filtering or other criteria for selection for inclusion in the final tokenized dataset.\n",
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"\n",
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"#### If one's data is in other formats besides .loom or .h5ad, one can use the relevant tools (such as Anndata tools) to convert the file to a .loom or .h5ad format prior to running the transcriptome tokenizer.\n",
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"\n",
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"#### OF NOTE: PLEASE ENSURE THE CORRECT TOKEN DICTIONARY AND GENE MEDIAN FILE IS USED FOR THE CORRECT MODEL.\n",
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"\n",
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"#### The 95M model series also require the special_token argument to be set to True."
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