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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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Using counts from 'SCT' assay and 'data' slot for trajectory analysis #164

Closed reneemoerkens closed 1 year ago

reneemoerkens commented 1 year ago

Dear SCTransform development team,

After transforming my scRNAseq dataset using SCTransform v2 (according to the vignette: https://satijalab.org/seurat/articles/sctransform_v2_vignette.html), can I now use the count matrix from 'SCT' assay and 'data' slot for trajectory analysis (such as PAGA, scVelo, CellRank)?

Thank you!

saketkc commented 1 year ago

I think this question would be more suited to scVelo/CellRank authors.