DriesSchaumont
commented
9 months ago Hi @MatthiasBeyens, regarding 'add assignment of guides to cells to gdo modality obms layer of single sample' and 'add guide-cell transduction categorization functionality to gdo modality obs layer of single sample', could you explain this a bit more? Is there a tool or some code that provides this functionality?
Also, combining multiple samples is supported using the concat component. Could you explain if something is missing? If so, could you describe the missing feature please?
MatthiasBeyens
To enable gdo modality analysis from single h5mu or from multi sample integrated h5mu, the analyst requires more data to avoid cumbersome and error-prone post-processing within multi-sample context.
Therefore I suggest the following task to complete:
[x] feature_type must be gdo following best practices (https://github.com/openpipelines-bio/openpipeline/commit/b0e21b3b4715267055b2defbb147c7a9c5d0a7bd)
[x] bugfix var genome column name to gdo modality. Currently column name is present, but does not populate with genome string).
[x] add assignment of guides to cells to gdo modality obms layer of single sample
idea
df = sc.get.obs_df( mdata.mod['CRISPR Guide Capture'], keys = guides )- [ ] add guide-cell transduction categorization functionality to gdo modality obs layer of single sample- [ ] enable merge operation of gdo modality across multi samples of single sample[x] #491
[x] #493