Package: lipidr
Title: Data Mining and Analysis of Lipidomics Datasets
Version: 2.23.0
Authors@R: c(
    person(
        "Ahmed", "Mohamed", 
        email = "mohamed@kuicr.kyoto-u.ac.jp", role = "cre",
        comment = c(ORCID = "0000-0001-6507-5300")
    ),
    person(
        "Ahmed", "Mohamed", 
        email = "ahmed.mohamed@qimrberghofer.edu.au", role = "aut"
    ),
    person(
        "Jeffrey", "Molendijk", 
        email = "Jeffrey.Molendijk@qimrberghofer.edu.au", role = "aut"
    ))
Description: lipidr an easy-to-use R package implementing a complete workflow 
    for downstream analysis of targeted and untargeted lipidomics data. 
    lipidomics results can be imported into lipidr as a numerical matrix or
    a Skyline export, allowing integration into current analysis 
    frameworks. Data mining of lipidomics datasets is enabled through 
    integration with Metabolomics Workbench API. lipidr allows data inspection, 
    normalization, univariate and multivariate analysis, displaying informative
    visualizations. lipidr also implements a novel Lipid Set Enrichment 
    Analysis (LSEA), harnessing molecular information such as lipid class, 
    total chain length and unsaturation.
Depends: R (>= 3.6.0), SummarizedExperiment
Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
        tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD,
        magrittr
License: MIT + file LICENSE
Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling,
        testthat
VignetteBuilder: knitr
biocViews: Lipidomics, MassSpectrometry, Normalization, QualityControl,
        Visualization
Language: en-US
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
URL: https://github.com/ahmohamed/lipidr
BugReports: https://github.com/ahmohamed/lipidr/issues/
git_url: https://git.bioconductor.org/packages/lipidr
git_branch: devel
git_last_commit: 9ed2a4a
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 00:00:12 UTC; biocbuild
Author: Ahmed Mohamed [cre] (ORCID: <https://orcid.org/0000-0001-6507-5300>),
  Ahmed Mohamed [aut],
  Jeffrey Molendijk [aut]
Maintainer: Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
Built: R 4.5.0; ; 2025-06-05 13:17:52 UTC; windows
