A new approach to studying life in its environmental context
Geochemical biology represents evolution as a chemical process to better understand how genomes and proteomes react to environmental variation – from tumor microenvironments to microbial habitats in our bodies and on the Earth.

A geochemical toolkit for bioinformatics
canprot calculates oxidation state, hydration state, and other chemical metrics for proteins.
chem16S calculates chemical metrics for communities, linking genomes with environments. JMDplots contains code and data to reproduce many of the plots from my papers.

canprot

Chemical analysis of proteins

CRAN Downloads DOI GitHub
Documentation: canprot manual and these vignettes:
Demos for canprot
Introduction to canprot
More about metrics

chem16S

Chemical metrics for microbial communities

CRAN Downloads DOI GitHub
Read the chem16S paper in Bioninformatics
Documentation: chem16S manual and these vignettes:
Chemical metrics of reference proteomes for taxa
A chemical representation of genomic differences
Integration of chem16S with phyloseq
(Bioconductor package)
Plotting two chemical metrics
Find the thermodynamic components that matter for your communities

JMDplots

Plots from papers by Jeffrey M. Dick

DOI GitHub
Documentation: JMDplots manual and vignettes with links to full texts of papers.
Vignettes from recent publications are highlighted below.
Chemical analyses
Community-level chemical metrics for exploring genomic adaptation to environments (chem16S)
Adaptations of microbial genomes to human body chemistry (microhum) preprint
Influence of redox potential on bacterial protein evolution (orp16S)
Thermodynamic applications
Stability of carrollite (carrollite)
Geochemical information from genomes (utogig)
Water activity and redox potential in evolution and development (evdevH2O)
About

canprot, chem16S, and JMDplots are free software made available under the GPL. The maintainer of these packages is Jeffrey Dick. Please contact him at j3ffdick@gmail.com.

Last updated: 2024-03-25