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navinlabcode / copykat

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Any interests in making copyKat support python? #46

Closed hyjforesight closed 2 years ago

hyjforesight commented 2 years ago

Hello copykat, Thanks for developing this amazing package, which looks like working better than infercnv. We're wondering whether you're interested in making it support python? I saw the author of infercnvpy made the copykat function integrated into their package. Please check this https://github.com/icbi-lab/infercnvpy/pull/21. Thanks! Best, YJ

gaobio commented 2 years ago

Hello copykat, Thanks for developing this amazing package, which looks like working better than infercnv. We're wondering whether you're interested in making it support python? I saw the author of infercnvpy made the copykat function integrated into their package. Please check this icbi-lab/infercnvpy#21. Thanks! Best, YJ

Thank you @hyjforesight . It's a good idea of making a python version. But I need some free time... Leaving it open for now, may check the possibility of achieving this in summer...

grst commented 2 years ago

Hi @gaobio,

if you re-implement copyKAT in Python, I'd be happy to discuss integrating it into infercnvpy. There's already some functionality for annotating genomic positions and for visualizations that can be re-used for other algorithms than infercnv.

hyjforesight commented 2 years ago

happy to see @grst is here! Thanks @gaobio! I'm also from MD Anderson. Looking forward to the python version! It would be awesome!

gaobio commented 2 years ago

@hyjforesight @grst Actually, I did ask a student to work on this, but it was challenging to find the counterpart of several R packages in Python.

learnPandR commented 5 months ago

I really look forward to the python version. R is too slow when it deal with the large data.