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aertslab / AUCell

AUCell: score single cells with gene regulatory networks
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Run AUCell_buildRankings on HVG? #24

Closed aelhossiny closed 1 year ago

aelhossiny commented 2 years ago

Hi, thank you for such a wonderful tool,

I've an integrated dataset of ~121k cells with ~50k features, running AUCell_buildRankings() on this dataset keeps giving me that error

Error in asMethod(object) : 
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

I understand that this is a memory issue, can I run it on the top 2000 HVG as it's routinely done in other analyses? Or is it better to run it on individual samples separatly on whole genes?

s-aibar commented 1 year ago

Sorry, for questions on how to use the package, see: https://github.com/aertslab/AUCell/issues/26