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
git_url: https://git.bioconductor.org/packages/LIPIDIFy
git_branch: devel
git_last_commit: 69e5b67
git_last_commit_date: 2026-09-23
Repository: Bioconductor 3.24
Date/Publication: 2026-09-24
NeedsCompilation: no
Packaged: 2026-09-24 22:42:02 UTC; biocbuild
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>
Built: R 4.6.1; ; 2026-09-25 08:59:52 UTC; unix
