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caokai1073 / UnionCom

The Software of UnionCom Algorithm
MIT License
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Some questions about scNMT #5

Open TinyTigerPan opened 1 year ago

TinyTigerPan commented 1 year ago

Hi, thanks for your wonderful contribution. I have some questions about scNMT. If I want to use your package, what data format should I provide, and I want to know what its meaning? I notice README in scNMT mentioned data prepocess, but I can't find one end to end pipeline can be used. And such as mentioned proecess.py can't be find. I am not familiar with bioinfo, can you help me to understand or provide a data preprocess tutorial such as jupyter notebook. What I really want is how to used in my own data, can you help me? What data format should I prepared and how it be processed. Many thanks!

caokai1073 commented 1 year ago

Hi, thanks for your interest. Actually, the preprocess of scNMT here is not standard. What kind of data are you using? If you are working with single-cell sequencing data and looking for a standard preprocessing pipeline, I would recommend referring to our latest uniPort paper, which provides a comprehensive and widely accepted preprocessing pipeline using Scanpy. You can find more information on this preprocessing pipeline in the following link: https://uniport.readthedocs.io/en/latest/examples/PBMC/pbmc_integration.html#Data-preprocessing.