Vignettes from package JMDplots

aaaq		Amino acid group additivity (2006)
scsc		Yeast subcellular location (2009)
bison		Relative stabilities of proteins inferred from a hot-spring metagenome (2011 and 2013)
aoscp		Average oxidation state of carbon in proteins (2014)
cpcp		Chemical portraits of cancer proteomes (2016 and 2017)
chnosz10		CHNOSZ paper (2019)
chnosz10_SI		CHNOSZ supplementary plots (2019)
gradox		Carbon oxidation state of proteins inferred from metagenomes in redox gradients (2019)
gradH2O		Signatures of salinity gradients in the chemical composition of proteins (2020)
canH2O		Water as a reactant in the differential expression of proteins in cancer (2021)
mjenergy		Energy release during protein synthesis at ultramafic-hosted hydrothermal systems (2021) (full text)
evdevH2O		Water activity and redox potential in evolution and development (2022) (full text)
geo16S		Chemical links between redox conditions and community reference proteomes (2023) (full text)
utogig		Using thermodynamics to obtain geochemical information from genomes (2023) (full text)
orp16S		Influence of redox potential on bacterial protein evolution (2023)
chem16S		Community-level chemical metrics for exploring genomic adaptation to environments (2023)
carrollite		Stability of carrollite (2024)
microhum		Chemical features of proteins in microbial genomes (2025)

Supporting vignettes

Chemical analysis of differential expression data for the gradH2O paper:

Chemical analysis of differential expression data for the canH2O paper:

TCGA		The Cancer Genome Atlas
HPA		The Human Protein Atlas
yeast_stress		Yeast gene expression
breast, colorectal, liver, lung, pancreatic, prostate		Cancer vs normal tissue
hypoxia, secreted, osmotic_euk, glucose, 3D		Cell culture experiments

Vignettes in other packages

multi-metal

Diagrams with multiple metals in CHNOSZ (2021)