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qiime2 / q2-longitudinal

QIIME 2 plugin for paired sample comparisons
BSD 3-Clause "New" or "Revised" License
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Mirkat and PERMANOVA-S implementation #42

Open elong0527 opened 6 years ago

elong0527 commented 6 years ago

Improvement Description Just wondering if there are plan to implement the two methods below. They can also be used for longitudinal microbiome analysis with a given distance matrix.

References

  1. https://www.ncbi.nlm.nih.gov/pubmed/25957468
  2. https://academic.oup.com/bioinformatics/article/32/17/2618/2450751/PERMANOVA-S-association-test-for-microbial
nbokulich commented 6 years ago

both would be great additions — one problem is that both are only in R, so we would need to wrap the R packages in QIIME2 (this is possible; q2-dada2 is a good example).

Edit: looks like PERMANOVA-S (as part of the miLineage package) is actually in C, but wrapping would be similar to the R example.

elong0527 commented 6 years ago

I can try to implement the two tests in python after NMIT.

nbokulich commented 6 years ago

@elong0527 that would be awesome, thanks!

jairideout commented 6 years ago

It may be easier to wrap the R/C++ packages than re-implementing in Python. In addition to requiring less developer effort, we'd get access to upstream bug fixes, features, etc. implemented by the R/C++ package authors. Wrapping R or standalone binaries isn't really a problem, see q2-phylogeny and q2-alignment for examples of wrapping a standalone binary (e.g. FastTree, MAFFT) in QIIME 2.

The only limiting factor is that the R/C++ packages must be installable via conda (I don't know if those two packages are available as conda packages).