Sibyl is a package designed to test different rarefaction thresholds when normalizing microbial abundance data.
When performing Principal Component Analysis (PCA) and other types of ordination, it is necessary to make sure of choosing a rarefaction threshold which does not impact the structure of the data, or our conclusions, during exploratory analysis.
We recommend getting a working bioconductor installation through docker images for bioconductor. We find the use of containers very useful, allowing for isolation of R computing environments.
The bioconductor images are maintained and updated regularly, and already include all the necessary system dependencies to make Sibyl and all its dependencies work.
To get a container running fast use the following, it starts a R Studio server session which can be accessed at localhost:8787:
docker run \
-e DISABLE_AUTH=true \
-p 8787:8787 \
bioconductor/bioconductor_docker:latest
Then install the latest development version of Sibyl with:
BiocManager::install("Headonpillow/Sibyl",
dependencies = TRUE)
For Ubuntu/Debian run:
sudo apt update && sudo apt install -y \
libcurl4-openssl-dev libssl-dev cmake libxml2-dev build-essential \
liblapack-dev gfortran zlib1g-dev libgl1-mesa-dev libglu1-mesa-dev \
freeglut3-dev libx11-dev libjpeg-dev libpng-dev
Some package dependencies are hosted on Bioconductor. In order to install them
you will need to install {BiocManager}:
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install(version = "3.20")
BiocManager::install("remotes")Then it will be possible to install the latest development version of Sibyl with:
BiocManager::install("Headonpillow/Sibyl",
dependencies = TRUE)
The Sibyl package was created with the aim of testing the lower limit of rarefaction thresholds.
While microbial abundance data is slowly moving away from methods like rarefaction to account for differing library size, rarefaction has been extensively used and still in 2025 is present in much of the literature, and discussed.
When choosing a rarefaction threshold is common to need to operate a compromise between describing samples accurately (completeness), and including more samples, which might sometimes not meet the selected threshold.
Sibyl aims to solve that, allowing users to explore sample completeness, and the effect of rarefaction thresholds on ordinations, all with a single tool.