canprot: Compositional Analysis of Differentially Expressed Proteins in Cancer

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 references for all datasets.

Version:	1.0.0
Depends:	R (≥ 3.1.0)
Imports:	CHNOSZ (≥ 1.3.0), xtable, MASS, knitr, rmarkdown
Suggests:	KernSmooth
Published:	2020-05-11
Author:	Jeffrey Dick [aut, cre], Ben Bolker [ctb]
Maintainer:	Jeffrey Dick <j3ffdick at gmail.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL:	http://github.com/jedick/canprot
NeedsCompilation:	no
Citation:	canprot citation info
Materials:	README NEWS
CRAN checks:	canprot results

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