Date: 2020-08-02
Package: canprot
Version: 1.0.1
Title: Compositional Analysis of Differentially Expressed Proteins in Cancer
Authors@R: c(
    person("Jeffrey", "Dick", email = "j3ffdick@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-0687-5890")),
    person("Ben", "Bolker", role = "ctb",
      comment = c(ORCID = "0000-0002-2127-0443"))
    )
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Depends: R (>= 3.1.0)
Imports: CHNOSZ (>= 1.3.0), xtable, MASS, rmarkdown
Suggests: KernSmooth, knitr
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
  references for all datasets.
Encoding: UTF-8
License: GPL (>= 2)
BuildResaveData: no
VignetteBuilder: knitr
URL: http://github.com/jedick/canprot