DESCRIPTION

Package: PhosR
Type: Package
Title: A set of methods and tools for comprehensive analysis of phosphoproteomics data
Version: 1.13.1
Authors@R: c(
    person("Pengyi", "Yang", email = "pengyi.yang@sydney.edu.au", role = c("aut")),
    person("Taiyun", "Kim", email = "taiyun.kim91@gmail.com", role = c("aut")),
    person("Hani Jieun", "Kim", email = "jieun.kim@sydney.edu.au", role = c("aut")),
    person("Di", "Xiao", email = "di.xiao@sydney.edu.au", role = c("aut", "cre")))
Description: PhosR is a package for the comprenhensive analysis of phosphoproteomic data.
    There are two major components to PhosR: processing and downstream analysis.
    PhosR consists of various processing tools for phosphoproteomics data
    including filtering, imputation, normalisation, and functional analysis
    for inferring active kinases and signalling pathways.
License: GPL-3 + file LICENSE
Depends: R (>= 4.2.0)
Imports:
    ruv,
    e1071,
    dendextend,
    limma,
    pcaMethods,
    stats,
    RColorBrewer,
    circlize,
    dplyr,
    igraph,
    pheatmap,
    preprocessCore,
    tidyr,
    rlang,
    graphics,
    grDevices,
    utils,
    SummarizedExperiment,
    methods,
    S4Vectors,
    BiocGenerics,
    ggplot2,
    GGally,
    ggdendro,
    ggpubr,
    network,
    reshape2,
    ggtext,
    stringi
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: Software, ResearchField, Proteomics
Suggests:
    testthat,
    knitr,
    rgl,
    sna,
    ClueR,
    directPA,
    rmarkdown,
    org.Rn.eg.db,
    org.Mm.eg.db,
    reactome.db,
    annotate,
    BiocStyle,
    stringr,
    calibrate