TODO list for the paper

[VladimirShitov]

• ATAC
  • Work in progress: ATAC components #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
• Calibration script to make sure results are the same on different systems
• Interoperability with Open Problems

[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