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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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Integrating SCTransform-normalised data with LIGER #277

Open lucygarner opened 1 year ago

lucygarner commented 1 year ago

Related to #161, is it still necessary to manually ensure that the Pearson residuals are non-negative in order to use SCTransform-normalised data for LIGER?

Do I just start from RunOptimizeALS after running SCTransform? And would I run SCTransform with all batches combined or for each batch separately?

Is this tutorial up-to-date for the current version of LIGER?
http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/liger.html

Thanks!

cblazier commented 1 year ago

I would also like to know whether I can use SCTransform on my data before starting with the Seurat-to-LIGER pipeline, and whether I should do it on samples separately or combined!