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Scanpy has documentation where mitochondrial genes could be easily filtered out using ["MT"]. I was wondering if anybody has information on whether there's a similar method for nuclear genes. My dataset will be using nRNA expression as a filter rather than MT. Thank you in advance.

  • $\begingroup$ nRNA = nuclear RNA? what is your objective? typical scanpy workflow filters cells that have high % mitocondrial counts, rather than filtering the actual genes $\endgroup$ Jul 3 at 17:26

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