DESCRIPTION

Package: protti
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Version: 0.9.1
Authors@R: 
    c(person(given = "Jan-Philipp",
           family = "Quast",
           role = c("aut", "cre"),
           email = "quast@imsb.biol.ethz.ch",
           comment = c(ORCID = "0000-0003-2713-778X")),
	person(given = "Dina",
           family = "Schuster",
           role = c("aut"),
           email = "dschuster@ethz.ch",
           comment = c(ORCID = "0000-0001-6611-8237")),
	person(given = "ETH Zurich",
           role = c("cph", "fnd")))
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: 
Imports: 
    rlang, 
    dplyr, 
    stringr, 
    magrittr, 
    data.table, 
    janitor, 
    progress, 
    purrr, 
    tidyr, 
    ggplot2, 
    forcats, 
    tibble, 
    plotly,   
    ggrepel, 
    utils,
    grDevices,
    curl,
    readr,
    lifecycle,
    httr,
    methods,
    R.utils,
    stats
RoxygenNote: 7.3.2
Suggests: 
    testthat,
    covr,
    knitr,
    rmarkdown,
    shiny,
    r3dmol,
    proDA,
    limma,
    dendextend,
    pheatmap, 
    heatmaply,
    furrr, 
    future, 
    parallel,
    seriation,
    drc,
    igraph,
    stringi, 
    STRINGdb,
    iq,
    scales,
    farver,
    ggforce,
    xml2,
    jsonlite
Depends: 
    R (>= 4.0)
URL: https://github.com/jpquast/protti, https://jpquast.github.io/protti/
BugReports: https://github.com/jpquast/protti/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)