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immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony
https://portals.broadinstitute.org/harmony/
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How to obtain harmony count matrix? #182

Closed adelpinoherrera closed 11 months ago

adelpinoherrera commented 1 year ago

Hello,

I am working with single-cell RNA sequencing data and I want to obtain a count matrix that shows my cells on either the rows or columns and the genes on either the rows or columns and the corrected counts for those based on the harmony batch effect reduction. I was wondering if this was possible.

Thank you

gaze-abyss commented 1 year ago

I also want to get the matrix after batch correction, both count and expression are fine.

pati-ni commented 11 months ago

Harmony is designed to correct cell embeddings. Therefore, it is not possible to correct the gene expression matrix. While you can provide scaled gene values, it is not guaranteed to provide best results.

Hope this addresses the question.