Imputation methods
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Description
@falexwolf, @flying-sheep
From the discussion on #45, I think some more discussion should be had as to what imputation methods are to be included in scanpy. Validation of and comparisons between the currently available imputation methods are both severely lacking---I only know of [1][2][3][4][5], none of which include comprehensive benchmarks, and the updated MAGIC (#187) article at Cell doesn't include relevant comparisons between current methods.
I'd be very interested in hearing/having an open discussion about the motivation, benefits, and limitations of the various imputation methods available.
[1]: Zhang and Zhang, 2017. https://www.biorxiv.org/content/early/2017/12/31/241190
[2]: Lopez et al. 2018, https://www.biorxiv.org/content/early/2018/03/30/292037
[3]: Li and Li, 2018. https://www.nature.com/articles/s41467-018-03405-7
[4]: Eraslan et al. 2018. https://www.biorxiv.org/content/early/2018/04/13/300681
[5]: Huang et al. 2018. https://www.biorxiv.org/content/early/2018/03/08/138677
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
No files, tests, or entry points are named. Start by reading discussion #45 and the cited papers, then review the current methods and the MAGIC work in #187. The issue needs agreement on which methods and comparisons are wanted before implementation can begin; its completion criteria are not defined.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100