Depends: R (>= 3.5.0), car, heplots (>= 0.8-6), graphics, stats

Title: Chemical Composition of Differential Protein Expression
Imports: CHNOSZ (>= 1.1.0), colorspace, xtable
Description: Datasets are collected here for differentially (up- and down-)
expressed proteins identified in proteomic studies of cancer and in cell
culture experiments. Tables of amino acid compositions of proteins are
used for calculations of chemical composition, projected into selected
basis species. Plotting functions are used to visualize the compositional
differences and thermodynamic potentials for proteomic transformations.

Title: Compositional Analysis of Differentially Expressed Proteins in
person("Jeffrey", "Dick", email = "j3ffdick@gmail.com", role = c("aut", "cre"),
Imports: CHNOSZ (>= 1.3.0), xtable, MASS, knitr, rmarkdown
Description: Compositional analysis of differentially expressed proteins in
cancer and cell culture proteomics experiments. The data include lists of up-
and down-regulated proteins in different cancer types (breast, colorectal,
liver, lung, pancreatic, prostate) and laboratory conditions (hypoxia,
hyperosmotic stress, high glucose, 3D cell culture, and proteins secreted in
hypoxia), together with amino acid compositions computed for protein sequences
obtained from UniProt. Functions are provided to calculate compositional metrics
including protein length, carbon oxidation state, and stoichiometric hydration
state. In addition, phylostrata (evolutionary ages) of protein-coding genes are
compiled using data from Liebeskind et al. (2016) <doi:10.1093/gbe/evw113> or
Trigos et al. (2017) <doi:10.1073/pnas.1617743114>. The vignettes contain
plots of compositional differences, phylostrata for human proteins, and

Suggests: CHNOSZ (>= 1.3.0), knitr, testthat

Title: Chemical Metrics of Differentially Expressed Proteins
Description: Chemical metrics of differentially expressed proteins in cancer
and cell culture proteomics experiments. Data files in the package have amino
acid compositions of proteins obtained from UniProt and >250 published lists of
up- and down-regulated proteins in different cancer types and laboratory
experiments. Functions are provided to calculate chemical metrics including
protein length, grand average of hydropathicity (GRAVY), isoelectric point
(pI), carbon oxidation state, and stoichiometric hydration state; the latter
two are described in Dick et al. (2020) <doi:10.5194/bg-17-6145-2020>. The
vignettes visualize differences of chemical metrics between up- and
down-regulated proteins and list literature references for all datasets.