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example `cell_type_train_data.dataset`?

#21
by AaronNing - opened
Discussion
AaronNing
•
edited Jun 8, 2023

Hi,
Great work! I am willing to use Geneformer right now. Do you have any plans on uploading an example "/path/to/cell_type_train_data.dataset" file, or/and providing a tutorial on how to convert standard single cell count data into a valid dataset to feed into Geneformer?
Thanks!

update: Sorry I missed the closed discussions on this. Now I just want to know whether this is on the plan, since I see you are actively updating the repo! : )
jinbo1129

same here
ctheodoris
 Owner

Thank you for your interest in Geneformer.

Regarding the example input files: please see the updated discussion in the closed issue https://huggingface.co/ctheodoris/Geneformer/discussions/16.

Regarding how to tokenize datasets with the transcriptome tokenizer, we added an example here: https://huggingface.co/ctheodoris/Geneformer/tree/main/examples
ctheodoris changed discussion status to closed
AaronNing

Thank you for your interest in Geneformer.

Regarding the example input files: please see the updated discussion in the closed issue https://huggingface.co/ctheodoris/Geneformer/discussions/16.

Regarding how to tokenize datasets with the transcriptome tokenizer, we added an example here: https://huggingface.co/ctheodoris/Geneformer/tree/main/examples

Thanks!

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