wejlab/animalcules

Import from phyloseq?

Closed this issue · 3 comments

cjfields commented

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

jasonzhao0307 commented

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

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

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