DESCRIPTION

Package: einprot
Type: Package
Title: A collection of proteomics analysis utilities and workflows
Version: 0.9.5
Authors@R: c(
    person("Charlotte", "Soneson", email = "charlotte.soneson@fmi.ch", 
           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3833-2169")),
    person("Jan", "Seebacher", role = "aut"),
    person("Michael", "Stadler", email = "michael.stadler@fmi.ch", 
           role = "aut", comment = c(ORCID = "0000-0002-2269-4934")),
    person("Tobias", "Kockmann", role = "ctb"),
    person("Friedrich Miescher Institute for Biomedical Research", 
           role = c("cph")))
Description: The einprot package contains utilities for performing analysis 
    of proteomics data. It provides end-to-end analysis workflows for data 
    quantified using MaxQuant, FragPipe and Proteome Discoverer. It also has 
    functionality for assembling databases of known protein complexes. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.0)
Imports: 
    babelgene,
    circlize,
    ComplexHeatmap,
    cowplot,
    dplyr,
    DT,
    genefilter,
    ggiraph,
    ggplot2 (>= 3.4.0),
    grDevices,
    ggrepel,
    imputeLCMD,
    IRanges,
    iSEEu,
    kableExtra,
    limma,
    mclust,
    methods,
    MsCoreUtils,
    msigdbr,
    plotly,
    QFeatures (>= 1.14.0),
    readr,
    rlang,
    rmarkdown,
    rrcovNA,
    S4Vectors,
    scales,
    scater,
    SingleCellExperiment,
    stats,
    STRINGdb,
    stringr,
    SummarizedExperiment,
    tibble,
    tidyr,
    utils,
    xfun,
    XML,
    xml2,
    ExploreModelMatrix,
    ComplexUpset,
    htmltools,
    knitr,
    proDA,
    forcats,
    ggalt,
    BiocSingular,
    tidyselect,
    GGally,
    scuttle,
    stringdist,
    shiny,
    writexl,
    tools,
    grid,
    Biostrings,
    motifStack
RoxygenNote: 7.3.2
Suggests: 
    BiocManager,
    testthat (>= 3.0.0),
    iSEE,
    matrixStats
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: Proteomics, DataImport