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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Find Variable Features in Signac #304

Closed sylestiel closed 3 years ago

sylestiel commented 3 years ago

Hi,

Is it practical to run Find Variable Features when analysing scATAC seq data in Signac.

Do we still use vst for that purpose. What is the recommended nfeatures for the same?

Thanks,

timoast commented 3 years ago

No, the concept of "mean expression" doesn't make sense for scATAC-seq. We typically use all peaks open in some minimum number of cells. See the FindTopFeatures() function