Open elong0527 opened 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.
I can try to implement the two tests in python after NMIT.
@elong0527 that would be awesome, thanks!
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).
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