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wejlab / animalcules

R shiny app for interactive microbiome analysis
https://wejlab.github.io/animalcules-docs/
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Import from phyloseq? #38

Closed cjfields closed 3 years ago

cjfields commented 5 years ago

Just a quick question on whether importing data from phyloseq instances is a possibility.

jasonzhao0307 commented 5 years ago

We currently don't have functions taking phyloseq objects into animalcules directly, but you could extract the count matrix and taxonomy table from phyloseq and upload to animalcules using the "count file" option

jasonzhao0307 commented 4 years ago

Now animalcules support BIOM data input, so phyloseq users could firstly get BIOM from phyloseq object, and then upload BIOM to animalcules. Note that, the BIOM file must contain sample metadata information, if not, please add metadata info to the BIOM file via: http://biom-format.org/documentation/adding_metadata.html

jasonzhao0307 commented 3 years ago

We added a section in the Data Upload tutorial on how to import phyloseq object: https://compbiomed.github.io/animalcules-docs/articles/rmd/upload.html