search

qiime2 / q2-composition

BSD 3-Clause "New" or "Revised" License
5 stars 27 forks source link

NEW: add ancombc2 to composition #132

Open lizgehret opened 6 months ago

lizgehret commented 6 months ago

Now that the ancombc2 paper has been published, it would be nice to add this method into q2-composition. @FrederickHuangLin we'd love to collaborate with you on this in any way that seems reasonable to you - how would you feel about us adding this into q2-composition at some point in the near future? Do you have any requests/thoughts/concerns about this?

FrederickHuangLin commented 6 months ago

Hi @lizgehret,

Thank you for reaching out! I hope your new year is off to a great start!

I recently had a conversation with Greg regarding this potential collaboration. It would be fantastic if you could assist in adding ancombc2 to the q2-composition plug-in. Please let me know how I can assist you with this endeavor.

Additionally, we're more than happy to provide a tutorial for ancombc and ancombc2, similar to other plug-ins, if that could help QIIME2 users. Starting next year, I'll have some of my students monitoring the QIIME2 discussion forum for ancombc-related topics.

Furthermore, I wanted to inquire about the potential addition of our methodology for microbial correlations, SECOM, to QIIME2. You can find more information about SECOM here. Would this be of interest to your team?

lizgehret commented 4 months ago

Hi @FrederickHuangLin,

Apologies for the delayed response here! I'm just getting caught up on things after some vacation and travel for work.

I recently had a conversation with Greg regarding this potential collaboration. It would be fantastic if you could assist in adding ancombc2 to the q2-composition plug-in. Please let me know how I can assist you with this endeavor.

That's great! It's looking like this might be something that @cherman2 will be working on in the near future. We'll follow up with you once we are ready to start working on this and if we run into any questions or concerns on that front.

Additionally, we're more than happy to provide a tutorial for ancombc and ancombc2, similar to other plug-ins, if that could help QIIME2 users. Starting next year, I'll have some of my students monitoring the QIIME2 discussion forum for ancombc-related topics.

I did update the sections of our existing tutorials that were using ANCOM to now include ANCOM-BC - you can check them out here:

Moving Pictures Parkinson's Mouse

I'm sure we'd be happy to have a more in-depth tutorial on ANCOM-BC added to our list of method-specific tutorials if your team is up for that! We do get a decent number of ANCOM-BC related questions, so I'm sure a more detailed tutorial would be really helpful for users.

Furthermore, I wanted to inquire about the potential addition of our methodology for microbial correlations, SECOM, to QIIME2. You can find more information about SECOM here. Would this be of interest to your team?

That's a great question! I know we had talked about adding this a while back (in addition to ANCOM-BC), but I'll bring this to our team meeting this week to see if this is something we have bandwidth for. I'll circle back with you after discussing with Greg and the rest of the team!