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Implementing differential abundance analysis #40

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khemlalnirmalkar opened this issue Apr 13, 2022 · 2 comments
Open

Implementing differential abundance analysis #40

khemlalnirmalkar opened this issue Apr 13, 2022 · 2 comments
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enhancement New feature or request

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@khemlalnirmalkar
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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
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sbslee commented Apr 13, 2022

@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.

@sbslee sbslee changed the title differential abundance Implementing differential abundance analysis Apr 13, 2022
@sbslee sbslee added the enhancement New feature or request label Apr 13, 2022
@khemlalnirmalkar
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Oh, okay, sounds great,
Thanks

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@sbslee @khemlalnirmalkar