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Accomplishments at the inaugural Hack-a-thon

Present: Hector with lab members Jay and Nate, Levi and Marcel, and Joey McMurdie remotely)

• Defined the MicrobiomeExperiment class. Contains SummarizedExperiment but requires a MicrobiomeFeatures class rowData. MicrobiomeFeatures contains metagenomeFeatures defined in the mgFeatures package with added constructor. It contains DataFrame and adds slots for a phylo-class tree and sequences.
• Constructor
• Coercion for phyloseq objects
• Some unit tests
• Coercion for MRExperiment objects (from metagenomeSeq)
• Import from biom files (using biomformat package) into MicrobiomeExperiment objects

TODO

• Move MicrobiomeFeatures to MicrobiomeExperiment package (Nate)
• Data import
• Tree based aggregation, pruning
• phylo and MicrobiomeFeatures extractors
• See phyloseq-basics vignette, implement functions not synonymous with SummarizedExperiment alternatives
• Make a phyloseq cheat sheet that Joey can use for migration
• Look at adephylo package
• See issues on HCBravoLab/MicrobiomeExperiment