inst/explore-anacapa-output/docs/download-text-phyloseq.md

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

You can conver this file into to a BIOM file using the following command in the terminal (assuming you have the biom software installed; see here for installation instructions):

biom convert --to-hdf5 --table-type="OTU table" -i taxonomy-for-biom.txt -o taxonomy-as-biom.biom

Once converted, the BIOM file can be imported into QIIME2 using the steps outlined at this page.

Download taxonomy table for downstream analysis as a phyloseq object

You can also download your taxonomy table as a Phyloseq object for downstream analyses in R. You can import this phyloseq object into R using the following command:

phyloseq_obect <- readRDS("phyloseq-object.Rds")

gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.