├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── Dockerfile ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS ├── R ├── annotation.R ├── bioc.R ├── check_files.R ├── de-analysis.R ├── impute.R ├── lipidr-package.R ├── lsea.R ├── manip.R ├── mva.R ├── mw.R ├── normalize.R ├── plot.R ├── readfiles.R ├── summarize.R ├── utils-df.R ├── utils-misc.R ├── utils-pipe.R └── utils-workflow.R ├── README.md ├── codecov.yml ├── data-raw ├── data_normalized.R └── lipidnames_pattern.R ├── data ├── data_normalized.rda ├── lipidDefaults.rda └── lipidnames_pattern.rda ├── docs └── CNAME ├── inst ├── WORDLIST └── extdata │ ├── A1_data.csv │ ├── F1_data.csv │ ├── F2_data.csv │ ├── brca_clin.csv │ ├── brca_matrix.csv │ └── clin.csv ├── man ├── LipidomicsExperiment-class.Rd ├── LipidomicsExperiment.Rd ├── add_sample_annotation.Rd ├── annotate_lipids.Rd ├── as_lipidomics_experiment.Rd ├── data_normalized.Rd ├── de_analysis.Rd ├── figures │ ├── logo.png │ ├── num_matrix.png │ ├── skyline_export.png │ └── workflow.png ├── filter_by_cv.Rd ├── gen_lipidsets.Rd ├── impute_na.Rd ├── lipidDefaults.Rd ├── lipidnames_pattern.Rd ├── lipidr-data.Rd ├── lipidr-package.Rd ├── lsea.Rd ├── mva.Rd ├── mw.Rd ├── non_parsed_molecules.Rd ├── normalize_istd.Rd ├── normalize_pqn.Rd ├── pipe.Rd ├── plot_chain_distribution.Rd ├── plot_lipidclass.Rd ├── plot_molecules.Rd ├── plot_samples.Rd ├── plot_trend.Rd ├── read_skyline.Rd ├── remove_non_parsed_molecules.Rd ├── set_attr.Rd ├── summarize_transitions.Rd ├── update_molecule_names.Rd └── use_interactive_graphics.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── spelling.R ├── testthat.R └── testthat │ ├── A1.csv │ 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