run `ddqc` on aggregated dataset or sample by sample ?

ayshwaryas / ddqc

Biology-centered data-driven quality control for scRNA-seq

BSD 3-Clause "New" or "Revised" License

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run `ddqc` on aggregated dataset or sample by sample ? #3

Open hl-xue opened 1 year ago

hl-xue commented 1 year ago

Hello,

Thanks for developing this software, I have a question about its usage please: I noticed that the workflow does not contain a batch correction step between PCA and neighbourhood graph construction. So I was wondering if the dataset is composed by multiple samples, should I run ddqc on the aggregated dataset or in a sample-by-sample fashion?

Thanks.

YiweiNiu commented 9 months ago

Hi, also interested in this question.