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nf-core / scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable
https://nf-co.re/scdownstream
MIT License
44 stars 12 forks source link

Implement integration benchmarking using scIB #13

Open nictru opened 5 months ago

nictru commented 5 months ago

Description of feature

Users should be able to systematically evaluate the quality of the created integrations. scIB seems like the most suitable tool for this. Has already been implemented in SIMBA. Results should be added to the MultiQC report.

ryan2han commented 1 month ago

When using the integration benchmark with scIB, it requires a label_key. Will users need to prepare their own annotations in advance, or can we utilize the cell-type labels from celltypist as the label_key?

nictru commented 1 month ago

I think both options can easily be implemented, so I will probably add a parameter for selection.

nictru commented 1 month ago

Can be based on the implemenation from here