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EcoJulia / Microbiome.jl

For analysis of microbiome and microbial community data
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support for biom format? #113

Open aguang opened 2 years ago

aguang commented 2 years ago

Will there be support for the biom format eventually?

kescobo commented 2 years ago

I think it would be really nice - I had that as a stretch goal at one point. I think it should be possible (probably as a stand-alone package) using HDF5.jl.

One idea I had was, something that reads a .biom file and can spit out the OTU table and the metadata as separate Tables.jl - compatible tables, then one could do something like

biom = read_biom("somefile.biom")
cmp = CommunityProfile(otus(biom))
insert!(cmp, metadata(biom))
aguang commented 2 years ago

I think that would be really cool. I will hopefully be bringing on a student to work on some microbiome data I will be getting soon, that might be something we could work on as part of it.

kescobo commented 2 years ago

That would be great! It's not a high priority for me to work on on my own, but I'd be more than happy to help someone else with code review / suggestions etc.