TPM instead of count data & no conditions

rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

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TPM instead of count data & no conditions #22

Closed nicholascwho closed 4 years ago

nicholascwho commented 4 years ago

Hi @rezakj

Thank you for this great resource! I was just wondering, if I only have TPM data instead of count data, would that be okay for make.obj()?

Also, if I have no conditions like in example 1, how would I use data.aggregation()? And would it affect the later function calls?

Thanks!

rezakj commented 4 years ago

Yes, you can use iCellR. If you already have normalized the data skip the normalization step.

If you have only one sample skip the aggregation step.

nicholascwho commented 4 years ago

Okay, thank you so much!