scTransform support

[mikecuoco]

Hi @bli25 et al.,

Thank you for developing this incredible toolkit! Is has saved our team so much time and effort in our single-cell analysis workflow. We are very interested in using an scTransform-like approach to normalize the raw counts in-place of log_norm. Have you considered adding a scTransform function for normalization?

It looks like there are some python implementations out there:

https://github.com/saketkc/pysctransform
https://github.com/atarashansky/SCTransformPy
https://github.com/deto/SCTransformPy

Mike

[mikecuoco]

@yihming I'd be happy to implement this! Could I put it in tools/preprocessing.py?

[yihming]

Hi @mikecuoco . You're more than welcomed to contribute to pegasus with the methods you think are useful. Yes, tools/preprocessing.py would be the appropriate place to go since this approach works on log-norm step.

Thank you for your interest to help!

Sincerely,
Yiming