Allow alternative clustering

JonathanShor / DoubletDetection

Doublet detection in single-cell RNA-seq data.

https://doubletdetection.readthedocs.io/en/stable/

MIT License

85 stars 23 forks source link

Allow alternative clustering #120

Closed adamgayoso closed 2 years ago

adamgayoso commented 5 years ago

We should allow any clustering method to be used (either through scanpy or an alternative)

adamgayoso commented 5 years ago

This will not be implemented in 3.0. We instead use built in scanpy clustering, or PhenoGraph.

kanefos commented 3 years ago

Hi authors, really smart tool with great documentation, having a blast. Thought I'd reply on this topic: just wondering if you have any thoughts on using the Leiden versus Louvain algorithm for the BoostClassifier's _.one_fit method (line 325, replaced sc.tl.louvain with c.tl.leiden. Ta!

adamgayoso commented 3 years ago

We can certainly add this as an option, but probably throw a user warning that it's experimental. We also need to give access to the resolution param.