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lilab-bcb / pegasus

A tool for analyzing trascriptomes of millions of single cells.

Home Page:https://pegasus.readthedocs.io

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scTransform support

mikecuoco opened this issue · comments

commented

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