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Implement integration benchmarking using scIB #13

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nictru opened this issue Jun 13, 2024 · 3 comments
Open

Implement integration benchmarking using scIB #13

nictru opened this issue Jun 13, 2024 · 3 comments
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enhancement New feature or request

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@nictru
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nictru commented Jun 13, 2024

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.

@nictru nictru added the enhancement New feature or request label Jun 13, 2024
@nictru nictru added this to the Stable transcriptomics milestone Jun 13, 2024
@ryan2han
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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
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nictru commented Oct 20, 2024

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

@nictru
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nictru commented Oct 28, 2024

Can be based on the implemenation from here

@manogenome manogenome self-assigned this Oct 28, 2024
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