Add Galaxy tutorial for breast cancer spatial transcriptomics analysis from Galaxy-EISTA - #7025
Add Galaxy tutorial for breast cancer spatial transcriptomics analysis from Galaxy-EISTA#7025khaled196 wants to merge 25 commits into
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khaled196
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…utorial.md Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
nilchia
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Thanks a lot @khaled196
Please also include the generated images in the training as well.
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Please change the "signals" from italic to normal.
The text in the box is outside of the box.
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Thanks for changing. The genes should be italic. They are human genes, right?
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Yes those are human genes. I removed them for now until find better annotating method.
…utorial.md Co-authored-by: Amirhossein Nilchi <66441226+nilchia@users.noreply.github.com>
…utorial.md Co-authored-by: Amirhossein Nilchi <66441226+nilchia@users.noreply.github.com>
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@nilchia Thank you, Amir, for your comments. Please check the tutorial again to see if I have addressed the comments. I will run it now on use.galaxy to see if I missed anything. |
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Are these two the only cell types in the data?
Can you please compare it to other papers/trainings using this data to check this?
thanks
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Thanks for changing. The genes should be italic. They are human genes, right?
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From this plot, I don't think there are only 2 cell types here
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I think the total count should be regressed out, no?
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Hi @khaled196, thank you again. I started to review again and made some comments, but now it seems to me that it is mainly AI-generated. In this case, I cannot review and correct your AI agent; this is something you should do. Please make this PR draft, review it yourself, and then mark it as ready for review only when you have really tested it (and also checked the rendering locally). For example, in the md file you are saying that 3 resolutions will be tested, and in the figure that you added, there are seven resolutions. |
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Thank you, @nilchia. I apologise for not reviewing the generated text carefully before pushing it. I left the manual validation until the end, which allowed several issues to remain. Regarding the CellTypist results, I need to investigate them further. My current understanding is that each Visium spot can contain transcripts from multiple cells, so the predicted labels should not be treated as pure cell identities or as a complete inventory of the cell types in the tissue. I have now revised the tutorial, tested the steps manually in Galaxy, and updated the repository. We can review any remaining points during our meeting later today. |
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Add Galaxy tutorial for breast cancer single cell analysis from Galaxy-EISTA