FIt-SNE integration?
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- Dominant language
- Python
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
...
Hi!
We're considering implementing some of the t-SNE recommendations in https://www.nature.com/articles/s41467-019-13056-x for our single-cell analysis. They use a different t-SNE implementation (https://github.com/KlugerLab/FIt-SNE), and before I ran off doing my own wrapping and plumbing to integrate with Scanpy I thought I'd check: have you considered integrating this yourselves?
Thanks!
Jon
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the sc.tools entry points and the cited FIt-SNE package, then compare the requested integration with the referenced t-SNE recommendations. Done requires an agreed scope for integrating FIt-SNE into Scanpy; the issue names no files or tests and leaves the implementation details open.
Written by the indexing model from the issue text.
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
- 25/100