Package: SmartPhos
Type: Package
Title: A phosphoproteomics data analysis package with an interactive ShinyApp
Version: 1.1.0
Authors@R: c(person("Shubham", "Agrawal", role = c("aut", "cre"), 
		email = "shubhamagrawal2706@gmail.com",
		comment = c(ORCID = "0009-0005-2630-9342")),
    person("Junyan", "Lu", role = c("aut"), 
		email = "jylu1118@gmail.com",
		comment = c(ORCID = "0000-0002-9211-0746")))
Description: 
    To facilitate and streamline phosphoproteomics data analysis, we developed
    SmartPhos, an R package for the pre-processing, quality control, and 
    exploratory analysis of phosphoproteomics data generated by MaxQuant and 
    Spectronaut. The package can be used either through the R command line or 
    through an interactive ShinyApp called SmartPhos Explorer. The package 
    contains methods such as normalization and normalization correction, 
    transformation, imputation, batch effect correction, PCA, heatmap, 
    differential expression, time-series clustering, gene set enrichment analysis,
    and kinase activity inference. 
License: GPL-3
biocViews: Visualization, ShinyApps, GUI, QualityControl, Proteomics,
    DifferentialExpression, Normalization, Preprocessing, GeneSetEnrichment,
    Clustering, GeneExpression, MassSpectrometry, BatchEffect
BugReports: https://github.com/Bioconductor/SmartPhos/issues
Imports:
    MultiAssayExperiment,
    SummarizedExperiment,
    data.table,
    shiny,
    shinythemes,
    shinyjs,
    shinyBS,
    shinyWidgets,
    parallel,
    DT,
    tools,
    stats,
    ggplot2,
    plotly,
    ggbeeswarm,
    pheatmap,
    grid,
    XML,
    MsCoreUtils,
    imputeLCMD,
    missForest,
    limma,
    proDA,
    decoupleR,
    piano,
    BiocParallel,
    doParallel,
    doRNG,
    e1071,
    magrittr,
    matrixStats,
    rlang,
    stringr,
    tibble,
    dplyr,
    tidyr,
    Biobase,
    vsn,
    factoextra,
    cowplot
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Depends: R (>= 4.4.0)
Suggests: 
    knitr,
    BiocStyle,
    PhosR,
    testthat
Config/testthat/edition: 3
URL: https://lu-group-ukhd.github.io/SmartPhos/
git_url: https://git.bioconductor.org/packages/SmartPhos
git_branch: devel
git_last_commit: 9abaf07
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
