Kruse, P. M. | Search bioRxiv

bioRxiv2025

treecompareR: Tree Visualizations of Chemical Space

This paper presents the treecompareR package for R, which provides tools for reproducible visualizations of data through the use of taxonomies. The package builds on developments from ggplot2 and ggtree to provide visualizations tailored for use with taxonomic classification data. Additionally, it provides tools that leverage developments in network analysis to compare data sets. While designed specifically for chemical classification objectives using ClassyFire (http://classyfire.wishartlab.com/), treecompareR also provides tools for use with more general taxonomies. treecompareR is available from GitHub at https://github.com/USEPA/treecompareR.

pharmacology and toxicology↗

bioRxiv2025

A Cheminformatics Workflow for Higher-throughput Modeling of Chemical Exposures from Biosolids

The U.S. Environmental Protection Agencys Biosolids Screening Tool can predict potential human and ecological exposures to chemical contaminants in treated sewage sludge biosolids, but large quantities of chemical-specific physico-chemical data are required to parameterize the model. Here, an R workflow is presented that leverages publicly-available databases of chemical information to prepare data for model simulations using the Biosolids Screening Tool. The automated Biosolids Screening Tool workflow (autoBST) reduces the time to gather data necessary to screen hundreds of chemicals from days to just a few minutes and provides transparent and reproducible data retrieval and input into existing models, allowing assessors to defensibly prioritize chemicals in biosolids that may pose a risk to human health or the environment.

pharmacology and toxicology↗