canprot

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 types of cancer (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) or Trigos et al. (2017). The vignettes contain plots of compositional differences, phylostrata (for human proteins), and references for all datasets.

For more information, see two papers in PeerJ (2016 and 2017).

Installation from CRAN

install.packages("canprot")

Installation from GitHub

First install the remotes package from CRAN:

install.packages("remotes")

Then install canprot from GitHub:

remotes::install_github("jedick/canprot")

This also installs other R packages as dependencies (particularly CHNOSZ, xtable, knitr and rmarkdown, and their dependencies).

Building vignettes

Building the vignettes requires pandoc to be available on the system. See rmarkdown's Install Pandoc vignette for tips on installing pandoc. With all the dependencies available, the vignettes can be compiled and viewed using the mkvig() function in canprot, like this:

library(canprot)
mkvig("3D")

Online vignettes

The vignettes can be viewed at http://chnosz.net/canprot/doc/index.html.