Wan Sze Cheng comments

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                                            Wan Sze Cheng

Proper steps for cellSNP and Vireo for large dataset

Hi things seems to work well now after using cellsnp-lite instead. Thanks!

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

@realzehuali May I ask how long it ended up taking? I am a similar size dataset and would like to have a better estimate of time. Thanks!

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

@saketkc Following up on this thread. I have once again an integration with 8 datasets, each with 10-50k cells, and the PrepSCTFindMarkers() function takes longer than 4 days already. If...

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

Thank you @saketkc for your reply. Could you clarify how to do it? I am not sure what do you mean by "rerun SCTransform for all objects separately". Thanks!

PrepSCTFindMarkers() is slow: "Recorrecting SCT counts using minimum median counts"

> ```r > ob.list ``` > > where is the minimum among the `median(ob$nCount_RNA)` among all your objects. I see what you mean, but like I mentioned before, my goal...