Implementing differential abundance analysis

sbslee / dokdo

A Python package for microbiome sequencing analysis with QIIME 2

https://dokdo.readthedocs.io

MIT License

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Implementing differential abundance analysis #40

Open khemlalnirmalkar opened 2 years ago

khemlalnirmalkar commented 2 years ago

Hi @sbslee I am curious to know, are differential analyses tools like lefse, ANCOM, ALDX2, and/or DeSeq2 for microbiota data out of scope for Dokdo? it would be wonderful to have them in Dokdo, if it is not possible, then never mind,

Thanks

sbslee commented 2 years ago

@khemlalnirmalkar,

Out of the aforementioned tools, I believe ANCOM is the only one that supports Python API via scikit-bio. Therefore, the other tools are in no doubt out of scope for Dokdo. I will consider implementing ANCOM for Dokdo, but it may take a while since it's not high priority. But as usual, thanks for the idea. I always welcome feature requests :) Please leave this issue open.

khemlalnirmalkar commented 2 years ago

Oh, okay, sounds great, Thanks