Submodule #88
Submodule #88
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:26Z Line #4. ) # "MT-" for human, "Mt-" for mouse please move the comment above the line for better formatting |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:26Z Is there a citation for the “permissive filtering” insight? If everything is explained in |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:27Z Looks like quite some overplotting. Maybe mention that this is not an ideal representation of the density of the samples? |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:28Z We throw a deprecation warning when not using it, right? Maybe mention that scanpy recommends using it. |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:29Z Why cluster before this?
ivirshup commented on 2024-03-22T21:25:14Z Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.
Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:30Z here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines) |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:30Z This part is confusing. You redefine the |
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View / edit / reply to this conversation on ReviewNB flying-sheep commented on 2024-03-22T10:33:31Z this is not a violin plot as advertised |
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Great new tutorial!
The only real issue is that there seems to be a reproducibility error around here: https://app.reviewnb.com/scverse/scanpy-tutorials/pull/88/discussion/#comment-2014799707
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Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.
Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.
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I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else. |
Making a doc update for scanpy 1.10. Includes some changes for this to better support being a gitsubmodule, though also makes a minor updates to docs.
see scverse/scanpy#2901