Application to sc epigenetic data

[ejc043]

Hello! Thanks for the great tool! I'm wondering about your thoughts on applying DCA to scATAC data?

[gabriele-gambero]

Hello! Thanks for the great tool! I'm wondering about your thoughts on applying DCA to scATAC data?

Hi @ejc043,

I managed to find it being used for spatial ATAC. However, after using it on the data derived from the study, I understood why they stated that it was applied only for "visualisation purposes": the denoising seems to reflect the difference in the sequencing depth, a common problem with ATAC, and you can clearly see it when performing clustering. Moreover, the LSI components have a different behaviour; usually, the first one is excluded, as it shows correlation with sequencing depth, while in this case, some other random PCs perform this way.
However, this might be related only to this spatial approach.

I hope this was useful!