Stress Microbiome "raw_format" Data (Greengenes)

Data from the Nephele-16S-Qiime-Greengenes microbiome pipeline in the form of a taxmap object. This taxmap object has been formatted into the MicrobiomeR "raw_format".

data(raw_greengenes)

Format

An object of class "Taxmap" with customized observation tables:

otu_abundance

An abundance table with otu_id, taxon_id, and Sample_* columns.

otu_annotations

A taxonomy annotations table with otu_id, taxon_id, and multiple rank columns.

sample_data

A metadata table with SampleID, BarcodeSequence, LinkerPrimerSequence, ForwardFastqFile, ReverseFastqFile, TreatmentGroup, SampleName, Description

phy_tree

A phylogenetic tree.

Source

Nephele-16S Qiime Pipeline

References

Zhang et al. (2019) (PubMed)