Input for batch-corrected data using Harmony

neurorestore / Augur

Cell type prioritization in single-cell data

MIT License

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Input for batch-corrected data using Harmony #10

Open danshu opened 3 years ago

danshu commented 3 years ago

Hi,

It is mentioned that harmony can be used for batch correction. However, harmony outputs batch-corrected PCs but not the gene-cell matrix. What should be the input in this case?

Best, Danshu

jordansquair commented 3 years ago

In this case you would want to use Harmony to obtain batch/condition corrected cell type annotations (which you would derive from your corrected PCs). You would then use these annotations as input to Augur, with the raw expression matrix.

vjbaskar commented 2 years ago

It would be nice if you can add this to the README. Thanks! Vijay