Package: LIPIDIFy
Type: Package
Title: Comprehensive Lipidomics Data Analysis with Interactive
        Visualization
Version: 0.99.7
Authors@R: c(
    person("Fayrouz", "Hammal", email = "fayrouz.hammal@petermac.org",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7612-4953")),
    person("Karen", "Sheppard", role = "fnd",
           comment = "NHMRC of Australia grant #2020050")
    )
Description: Provides a comprehensive toolkit for end-to-end lipidomics
        data analysis, including missing value imputation, batch effect
        correction, normalization, differential abundance analysis
        using limma and edgeR, gene set enrichment analysis, and
        extensive visualization capabilities. Lipid names are
        automatically classified by class, subclass, and fatty-acid
        saturation. Features both an interactive Shiny interface for
        bench biologists and fully scriptable R functions for
        bioinformaticians. Supports flexible custom lipid
        classification schemes and user-defined enrichment sets.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: shiny (>= 1.8.0), shinydashboard, ggplot2 (>= 3.5.0), ggrepel,
        plotly, DT, tidyr, dplyr, scales, gridExtra, grid, pheatmap,
        limma, edgeR, fgsea, FactoMineR, pls, openxlsx, rmarkdown,
        stringr, withr, utils, stats, grDevices
Suggests: BiocStyle, knitr, testthat (>= 3.0.0), impute, sva, vsn,
        SummarizedExperiment, tinytex, shinytest2, chromote
VignetteBuilder: knitr
biocViews: Software, Lipidomics, MassSpectrometry, Normalization,
        Preprocessing, DifferentialExpression, GeneSetEnrichment,
        Visualization, ShinyApps, MultipleComparison, BatchEffect,
        QualityControl, DataImport, Classification
URL: https://github.com/fayrouzhammal/LIPIDIFy
BugReports: https://github.com/fayrouzhammal/LIPIDIFy/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libfreetype6-dev make libicu-dev libpng-dev
        libuv1-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-23 11:16:50 UTC
RemoteUrl: https://github.com/bioc/LIPIDIFy
RemoteRef: HEAD
RemoteSha: 69e5b6746d59031024420a1bb6dbcdecbbfba5ad
NeedsCompilation: no
Packaged: 2026-10-26 11:47:25 UTC; root
Author: Fayrouz Hammal [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7612-4953>),
  Karen Sheppard [fnd] (NHMRC of Australia grant #2020050)
Maintainer: Fayrouz Hammal <fayrouz.hammal@petermac.org>