Package: SmartPhos
Type: Package
Title: A phosphoproteomics data analysis package with an interactive
        ShinyApp
Version: 1.0.0
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: RELEASE_3_22
git_last_commit: a7a52e6
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 04:13:50 UTC; biocbuild
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 4.5.1; ; 2025-10-30 09:41:48 UTC; unix
