Apply single cell QC and extract failed indices #39
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
d33bs
approved these changes
Feb 20, 2025
Member
d33bs
left a comment
d33bs
left a comment
There was a problem hiding this comment.
Good job - I left a few suggestions and overall thought this LGTM! Cheers on finding outliers using the tools we've built together within the lab on quite large datasets!
|
|
||
|
|
||
| # set a list of metadata columns for use throughout | ||
| metadata_cols = [ |
Member
There was a problem hiding this comment.
Consider including TableNumber also if it's available.
Member
Author
There was a problem hiding this comment.
I will add that back in! Do we know what TableNumber represents?
This was referenced Mar 3, 2025
Member
Author
|
@d33bs Thank you for the review! I am merging now! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Apply single-cell QC and extract failed indices
In this PR, coSMicQC processes the CytoTable JUMP pilot outputs and detects poor-quality segmentations. Indices for the failed single-cells are extracted as compressed CSVs for downstream processing.