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[kaizhang]

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[Chen-Li-17]

Hi kaizhang you really did a great job for snapatac used by python. And I'm wondering will you add more functions such as find highly variable peaks, linking enhancers to genes and scRNA-based annotation later? If so, what's the approximate time will be able to add them?

[Chen-Li-17]

And these functions have already implemented in snapATAC1.0, so I guess you may want to complete 2.0 like 1.0.

[kaizhang]

Hi kaizhang you really did a great job for snapatac used by python. And I'm wondering will you add more functions such as find highly variable peaks, linking enhancers to genes and scRNA-based annotation later? If so, what's the approximate time will be able to add them?

Yes, these features will be added gradually but I don't have a timeline for them with the exception that the identification of variable peak will be added soon.

[qinqian]

Is there a Python and Rust guideline to add codes into https://github.com/kaizhang/SnapATAC2/tree/main/snapatac2-contrib

[kaizhang]

Is there a Python and Rust guideline to add codes into https://github.com/kaizhang/SnapATAC2/tree/main/snapatac2-contrib

The reason for a separate snapatac2-contrib library is to give as much flexibility as possible to people to experiment with new snapatac2-related features. I don't want to put too many restrictions on that. The only suggestion is to put everything under the namespace snapatac2.contrib, followed by common categories like tl, pp, etc.

If you want to improve the existing features, you should contribute directly to the core libraries.

[qinqian]

Got it. Thanks!

[saraterzo]

Hi Kaizhang,
thank you for developing this very useful package. I was wondering, regarding the normalization of ATAC data, I couldn’t find any function for this purpose in the tutorial. What are your thoughts on this?
Best,
Sara

[kaizhang]

For the purpose of dimension reduction, the ATAC data does not need to be normalized. Our dimension reduction algorithm automatically normalize the data internally. For more details and benchmark, you can read our paper.

[saraterzo]

Thanks :)