McLaren MR, Willis AD, Callahan BJ. 2019. Consistent and correctable bias in metagenomic sequencing measurements. bioRxiv 559831. https://www.biorxiv.org/content/10.1101/559831v1

This repository is an R package. It can be installed or loaded without installation with devtools. Once loaded, all custom functions (defined in R/) used for our analysis will be available and all data objects used for our main statistical analyses (stored in data/) can be loaded with the data function.

The scripts we used to download and/or generate the necessary sample metadata, 16S and metagenomic taxonomic profiles, and taxon information for our analyses are in data-raw/. This folder also contains scripts that clean the data and save it as .rda (R data) objects that can be loaded with the data function once the R package is loaded. These objects serve as the starting point for subsequent analyses.

Analyses are contained in R-markdown documents in analysis/. Versions rendered to html can be seen at

• Analysis of the Brooks et al (2015) dataset
• Analysis of the Costea et al (2017) dataset
• Calculations for conceptual examples discussed in the manuscript

The vignettes/ folder contains a demonstration on simulated data of the bias estimation procedure we use in our main analysis. A rendered version can be found here.