Part I: Install R package “RioNorm2”

1.    Install the R packages “pscl", “phyloseq", “igraph", “MASS".

2.    Download the R package “RioNorm2” (it requires >= R3.5.1): 

·      Package source file: “RioNorm2.tar.gz”

·      Windows binaries: “RioNorm2.zip”

 

Part II: Tutorial on using “RioNorm2” for data analysis

1.    Please download the sample dataset “sample_data.csv”. It is a simulated dataset with 246 OTUs, 25 “class_0” samples and 25 “class_1” samples. The 30 OTUs with names ending with “-TP” have differential abundance between the two classes.

2.    Please download the R file “RioNorm2_On_sample_dataset.R” which shows the detailed steps using RioNorm2 package for the detection of differentially abundant OTUs between two groups.

 

Part III: Implementation of Simulation

For readers who want to try out the simulation studies performed in the paper, please download the following R files:

1.    “Simulation.R” : generate all the simulation data.

2.    “simulation_performance_comparison.R”:

·      Generate differential abundance analysis results for each of the methods: metagenomeSeq, DESeq, DESeq2, Omnibus, RAIDA, and RioNorm2.

·      Compare results using different methods under different simulation settings and visualize the results.