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Assistance Needed with Adding Cell-Type Column to h5ad File for scGPT Hub Submission #256

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msyed786 opened this issue Sep 19, 2024 · 1 comment

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@msyed786
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Hello!

We are currently trying to submit one of our lab's datasets (Input KYSE150_KDM4C_KO_Sensitivity#3) as an h5ad file to the scGPT Hub. However, in step three of the submission process, where we are asked to "Select the runtime parameters for your analysis," it requires a cell type input. Our dataset doesn't include a separate column for cell type, as it contains only human gene data, which leads to an error during the matrix validation process.

Could anyone advise how we can add a cell-type column to the dataset preferably using the tools provided by Galaxy Single Cell Omics or any other recommended methods, so that we can successfully submit our data for analysis?

Thank you for your help!

@miraclezero
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same here, how do we apply scgpt if no cell type column in h5ad obs?

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