Implement ANCOM, perhaps as part of differential_abundance.py

[colinbrislawn]

This recent paper presents Analysis of Composition of Microbiomes (ANCOM)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450248/

Congrats @wdwvt1, @rob-knight! I would love to see this method in qiime!

[wasade]

It's currently in an open PR scikit-bio/scikit-bio#1114; agree it would be
great to have available
On Oct 13, 2015 9:55 AM, "Colin Brislawn" notifications@github.com wrote:

This recent paper presents Analysis of Composition of Microbiomes (ANCOM)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450248/

Congrats @wdwvt1 https://github.com/wdwvt1, @rob-knight
https://github.com/rob-knight! I would love to see this method in qiime!

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#2090.

[colinbrislawn]

Excellent! The implementation itself does make more sense as part of skikit-bio, and this function can be added as a method in differential_abundance.py.

You can close this issue if you want.

[gregcaporaso]

There is a problem here unfortunately: QIIME 1 won't be updated to use a post 0.2.x version of scikit-bio, so this method won't be available. Unfortunately I think we'll have to wait for QIIME 2 to get moving if we're going to use the scikit-bio implementation (but it should be easy to use the scikit-bio implementation outside of QIIME once that PR is merged).

[ebolyen]

Technically speaking, there is no reason we couldn't backport ANCOM to a 0.2.4 release, but that isn't me volunteering...

[gregcaporaso]

Yep, it all comes down to what we have the bandwidth for. I'm really excited to start using this method, but I think the way to get there is to start focusing on QIIME 2 development.

[colinbrislawn]

I'm comfortable with this being incorporated into QIIME 2. If I need it before then, a colleague or I can run it through scikit-bio.

This is off topic, but what's the timeline for QIIME 2 release? Is your team planning a 1.10.0 release before 2.0.0? Just curious...

[gregcaporaso]

No, we're not planning a 1.10.0 release, but we will do bug fix 1.9.x
release if necessary. The plan is that 1.9.x is going to be a long-term
support release which we'll continue to support as we're developing,
releasing, and supporting early versions in the 2.x.x series of release. We
have a call coming up to discuss the plan for the 2.0.0 timeline, and we'll
share some information on that with the community after the call (we'll
post to the forum and the blog to indicate where that information can be
found).

On Tue, Oct 13, 2015 at 3:32 PM, Colin Brislawn notifications@github.com
wrote:

I'm comfortable with this being incorporated into QIIME 2. If I need it
before then, a colleague or I can run it through scikit-bio.

This is off topic, but what's the timeline for QIIME 2 release? Is your
team planning a 1.10.0 release before 2.0.0? Just curious...

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#2090 (comment).

[gregcaporaso]

In case folks haven't seen it, the blog post went up here.

[gregcaporaso]

ANCOM is now merged in scikit-bio, so will be included in the upcoming 0.4.1 release.