TODO list for the paper

[VladimirShitov]

• [ ] ATAC
  • Work in progress: https://github.com/openpipelines-bio/openpipeline/issues/398
• [ ] CCC analysis
  • Robrecht lift over from Open Problems?
• [ ] DE analysis
• [ ] Gene signatures
  • Janssen already started
• [ ] Composition analysis?
  • No benchmark yet, but there are some methods mentioned in the book (scCODA, MILO)
• [ ] Trajectories -> PAGA

[LuckyMD]

If we want to have major tasks from open pipelines covered in open problems, we would like:

• [ ] DE analysis
• [ ] Gene signature analysis
• [ ] Trajectory inference

ATAC:

• [ ] ATAC: preprocessing/featurization
• [ ] ATAC: dimensionality reduction / integration
• [ ] ATAC: differential accessibility analysis

Other:

• [ ] Better metrics (and methods) for multimodal integration (joint embedding), beyond NeurIPS 2021 competition

Priorities:

1. DE analysis
2. Multimodal integration
3. Trajectory inference