scRNA-seq data as input

[Qtasnim]

Hello,

I know this is meant for microarray and RNA-seq data, but is there a way to use this on scRNA-seq data if I transform it to RNA-seq-like dataframe??
Is it necessary to use raw datasets or can I use preprocessed data (counts after alignment) as input and skip the preprocessing steps?

Greatly appreciate any advice or suggestion.
Thank you.

[QingfeiPan]

Hi Qtasnim,

Thanks for your interest in NetBID!

1. Yes, you can directly use NetBID to analyze your scRNA-seq data.
2. If you start with raw counts (UMI counts for scRNA-seq data), you will need to: 1) filter out low-quality samples/cells; and 2) normalize and log-transform the data with log2(cpm+1) or any other methods you like. If your data is normalized and tranformed, you can skip the preprocessing step.

Please let me know if you have any other questions.

Best,
Qingfei