Package: PhosR
Type: Package
Title: A set of methods and tools for comprehensive analysis of
        phosphoproteomics data
Version: 1.20.0
Authors@R: c(
    person("Pengyi", "Yang", email = "pengyi.yang@sydney.edu.au", role = c("aut")),
    person("Di", "Xiao", email = "di.xiao@sydney.edu.au", role = c("aut", "cre")),
    person("Hani Jieun", "Kim", email = "jieun.kim@sydney.edu.au", role = c("aut")))
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: 7.2.2
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
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:02:33 UTC
RemoteUrl: https://github.com/bioc/PhosR
RemoteRef: RELEASE_3_22
RemoteSha: d795fca7330fdd460645cff9db6e819fa67b95d6
NeedsCompilation: no
Packaged: 2026-02-23 08:48:15 UTC; root
Author: Pengyi Yang [aut],
  Di Xiao [aut, cre],
  Hani Jieun Kim [aut]
Maintainer: Di Xiao <di.xiao@sydney.edu.au>
Built: R 4.5.2; ; 2026-02-23 08:51:39 UTC; windows
