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qiime2 / q2-composition

BSD 3-Clause "New" or "Revised" License
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update to ANCOM 2.0 #48

Closed gregcaporaso closed 2 years ago

gregcaporaso commented 6 years ago

Improvement Description The first author of the ANCOM paper, @sidhujyatha, has shared some R code with me which he would like to get wrapped in a QIIME 2 plugin, so we can support the latest version of ANCOM (ANCOM 2.0). This would be great to get in place, but we just need someone to take on wrapping this R script in a QIIME 2 plugin.

gregcaporaso commented 6 years ago

@FrederickHuangLin is interested in working with us on this plugin, so we should follow up once we're ready to get this plugin updated.

gregcaporaso commented 6 years ago

I have an updated version of this R code now, which was emailed to me by @sidhujyatha on 26 Jan 2018.

timyerg commented 5 years ago

Hi! The latest Qiime2 release already updated to ANCOM-2.0? I read your post on Qiime2 forum regarding features with low W or W = 0

thermokarst commented 5 years ago

Hi @timyerg, no, we have not yet added ANCOM 2 to this plugin.

timyerg commented 5 years ago

Thank you for the reply. I am @timanix, btw. I downloaded the file for R that Mehrbod_Estaki shared on the forum, but I am not sure that I can use it since it wasn't provided to me by the authors and I cannot find any website with the source and references...

mestaki commented 5 years ago

Hi @timyerg ,

Thank you for the reply. I am @timanix, btw. I downloaded the file for R that Mehrbod_Estaki shared on the forum, but I am not sure that I can use it since it wasn't provided to me by the authors and I cannot find any website with the source and references...

A bit late to this part, but just for reference, the source code that I linked to on the forum comes from the author's (Dr. Mandal) person page here.

lizgehret commented 2 years ago

Circling back on this for posterity - closing out this PR since we are currently working on adding ANCOM-BC in place of adding ANCOM 2 into q2-composition. This should be released in the November 2022 update, so stay tuned!

Development branch Working PR