canprot

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). The vignettes visualize differences of chemical metrics between up- and down-regulated proteins and list literature references for all datasets.

Please use this citation for the package: Dick (2021).

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 xtable, knitr and rmarkdown, and their dependencies).

Building vignettes

The main vignette provides a brief introduction to the package. There are separate analysis vignettes for each dataset; these are not built when the packagke is installed.

Building the analysis vignettes requires pandoc to be available on the system. To compile one of the analysis vignettes and open it in your browser, use the mkvig() function in canprot, like this:

library(canprot)
mkvig("3D")

Online vignettes

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