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igrabski / sc-SHC

Significance analysis for clustering single-cell RNA-sequencing data
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Compatibility with integration methods #3

Closed lucia-ramirez closed 1 year ago

lucia-ramirez commented 1 year ago

Hi, I would like to use your algorithm but wanted to know the best practices for running it. Specifically, I have used SCVI to batch-correct my data, so I was wondering if the algorithm could use that or if I should I use counts and adjust for batch effect?

Thanks!

igrabski commented 1 year ago

Thanks for your question! The input should always be counts, so in this case, I would recommend inputting the counts and using the batch effect option. Unfortunately, because of this requirement, our approach is generally not compatible with most integration methods.