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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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About gene activity matirx of sample integration #296

Closed millersan closed 3 years ago

millersan commented 3 years ago

Hi Tim, thank you for this great package. Base on the vignettes of "scATAC-seq data integration", I have integrated the scATAC data across 2 samples. Then I have a question how to calculated the gene activity matrix of the integrated data? should I combined two sample fragment to caluculated the gene activity matirx?

If I follow the "PBMC scATAC-seq Vignette" using the "hm.integrated", which assay represent the "ACTIVITY", should I create the gene activity matirx again in the "sciPeaks" assay?

timoast commented 3 years ago

The GeneActivity() function can be run on a merged or non-merged object, it doesn't matter.