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/
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:38:54 UTC
RemoteUrl: https://github.com/bioc/SmartPhos
RemoteRef: HEAD
RemoteSha: 9abaf07e422a6c6cf3f199e441bec2c3eafbf036
NeedsCompilation: no
Packaged: 2026-01-23 07:36:52 UTC; root
Author: Shubham Agrawal [aut, cre] (ORCID:
    <https://orcid.org/0009-0005-2630-9342>),
  Junyan Lu [aut] (ORCID: <https://orcid.org/0000-0002-9211-0746>)
Maintainer: Shubham Agrawal <shubhamagrawal2706@gmail.com>
Built: R 4.6.0; ; 2026-01-23 07:40:14 UTC; windows
