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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Update ADT filtering sections #125

Closed sjspielman closed 1 year ago

sjspielman commented 1 year ago

Closes #124

This PR updates docs to reflect changes implemented for ADT filtering in scpca-nf v0.5.3. Changes were made to indicate that sometimes filtering fails if cleanTagCounts() cannot reliably determine cells to filter (I decided not to get into the weeds of why cleanTagCounts() might have decided this, just that it did). In this case, log-normalization is performed, and the SCE metadata will state No filter for the filtering method.

Please let me know if we think there are other spots where text needs updating, and whether the updates I've made here are clear, thanks!

sjspielman commented 1 year ago

I'm requesting @jashapiro for review here b/c I suspect you'll have some thoughts on it, but I know your schedule might be tight today! If so, glad to invite @allyhawkins to jump in :)

sjspielman commented 1 year ago

thanks for the review, @jashapiro! broadly agree with everything you've caught here, fixes incoming..

sjspielman commented 1 year ago

Your table edits helped me fine a couple more typos, but otherwise all good!

I don't know if this phrasing was intentional, but I hope it was and I love it. Luckily, still great even if freudian..