This site contains all the necessary scripts and a minimal set of data to reproduce the results (with different random numbers generated) in
Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses, in prep.
The exact results generated in the study can be found on Dryad once the manuscript goes to publication:
https://doi.org/10.5061/dryad.2rbnzs7p5
(Before that happens, a private link can be provided upon request.)
The scripts have been tested on Windows 10, macOS 11.4 (Big Sur) and Ubuntu 18.04.1 LTS with R 3.6.3.
The following package is required to run all the scripts: RasperGade16S,RasperGade,castor,ape,phyloseq,ggplot2,ggpubr,ggtree
To reproduce the results in the preprint on macOS or Linux systems, follow the instrucitons in
Microbiome/Instruction_Ubuntu.sh
For Windows users, the reproduction of all figures can be done by sourcing the scripts under Scripts/Figures_and_Tables/ in RStudio.