scaled or arcsinh-transformed expression for annotation?
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 20/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
Research direction
Start with the manuscript’s discussion of Figure 6 and the heatmap guidance for cluster annotation. Compare the stated use of scaled expression values with the question about arcsinh-transformed values; done would be a resolved, documented recommendation, but the issue names no implementation file or test.
Written by the indexing model from the issue text.
Description
Thank you for developing this excellent tool.
In the manuscript, it suggested to use the heatmap from Figure 6 to annotate clusters, but we have a question regarding the use of scaled expression values (0-1). Since this scaling can artificially inflate low-expression markers, would using arcsinh-transformed values be a more appropriate method for cluster annotation?
- Dominant language
- TypeScript
- Stars
- 1.4k
- Forks
- 61
- Avg merge
- 1d 15h
- Merged PRs (30d)
- 8
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