This code adds the cpa method. It is a major change since the method operates on single-cell data and outputs an h5ad that contains single-cell data and will have to be pseudobulked and run through limma to get the final output. I limited this PR to CPA, but I'd appreciate your ideas on how to best integrate it into run_benchmark.
Also, since this would take a while to run, it would be great if you could try to run it in any way possible on AWS, so that I can at least use the output to generate a plot or table to the camera ready version (all of the remaining steps should be easy enough for me to run locally)
A primary issue with this code is that since I cannot run docker on our cluster, I cannot test it on a similar environment to AWS.
Checklist before requesting a review
[x] I have performed a self-review of my code
Check the correct box. Does this PR contain:
[ ] Breaking changes
[x] New functionality
[x] Major changes
[ ] Minor changes
[ ] Bug fixes
[ ] Proposed changes are described in the CHANGELOG.md
Describe your changes
This code adds the cpa method. It is a major change since the method operates on single-cell data and outputs an h5ad that contains single-cell data and will have to be pseudobulked and run through limma to get the final output. I limited this PR to CPA, but I'd appreciate your ideas on how to best integrate it into run_benchmark.
Also, since this would take a while to run, it would be great if you could try to run it in any way possible on AWS, so that I can at least use the output to generate a plot or table to the camera ready version (all of the remaining steps should be easy enough for me to run locally)
A primary issue with this code is that since I cannot run docker on our cluster, I cannot test it on a similar environment to AWS.
Checklist before requesting a review
[x] I have performed a self-review of my code
Check the correct box. Does this PR contain:
[ ] Proposed changes are described in the CHANGELOG.md
[ ] CI Tests succeed and look good!