├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── pkgdown.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── batch_normalise.R ├── class_metaboprep.R ├── continous_power_plot.R ├── cramer_v.R ├── export.R ├── feature_describe.R ├── feature_summary.R ├── generate_report.R ├── imbalanced_power_plot.R ├── missingness.R ├── multivariate_anova.R ├── outlier_detection.R ├── pc_and_outliers.R ├── quality_control.R ├── read_metabolon.R ├── read_nightingale.R ├── read_olink.R ├── read_somalogic.R ├── run_metaboprep1.R ├── sample_summary.R ├── shiny_app.R ├── summarise.R ├── summary_metaboprep.R ├── total_peak_area.R ├── tree_and_independent_features.R ├── utils.R ├── variable_by_factor.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data-raw ├── dummy_data.R └── generate_example_olink_data.R ├── inst ├── extdata │ ├── comets_v1_example.xlsx │ ├── dummy_data.csv │ ├── dummy_features.csv │ ├── dummy_samples.csv │ ├── metaboanalyst_v1_example.csv │ ├── metabolon_v1.1_example.xlsx │ ├── metabolon_v1.2_example.xlsx │ ├── metabolon_v2_example.xlsx │ ├── nightingale_v1_example.xlsx │ ├── nightingale_v2_example.xlsx │ ├── olink_v1_example.txt │ └── somalogic_v1_example.adat └── rmarkdown │ └── templates │ └── qc_report │ ├── skeleton │ ├── 01_summary_raw_data.Rmd │ ├── 02_data_filtering.Rmd │ ├── 03_summary_filtered_data.Rmd │ ├── latex_styles.sty │ ├── metaboprep_workflow.png │ ├── skeleton.Rmd │ └── styles.css │ └── template.yaml ├── man ├── add_layer.Rd ├── available_data_formats.Rd ├── available_report_templates.Rd ├── batch_normalise.Rd ├── class_metaboprep.Rd ├── clean_names.Rd ├── continuous_power_plot.Rd ├── cramerV.Rd ├── eval.power.binary.imbalanced.Rd ├── eval.power.cont.Rd ├── export.Rd ├── export_comets.Rd ├── export_metaboanalyst.Rd ├── export_metaboprep.Rd ├── feature_describe.Rd ├── feature_summary.Rd ├── figures │ ├── README-example-1.png │ ├── README-pressure-1.png │ ├── README-treeplot-1.png │ ├── cheatsheet.png │ ├── logo.png │ └── metaboprep_workflow.png ├── find.PA.effect.sizes.2.sim.Rd ├── find.cont.effect.sizes.2.sim.Rd ├── generate_report.Rd ├── imbalanced_power_plot.Rd ├── missingness.Rd ├── multivariate_anova.Rd ├── outlier_detection.Rd ├── outliers.Rd ├── pc_and_outliers.Rd ├── quality_control.Rd ├── read_metabolon.Rd ├── read_nightingale.Rd ├── read_olink.Rd ├── read_somalogic.Rd ├── run_metaboprep1.Rd ├── sample_summary.Rd ├── shiny_app.Rd ├── summarise.Rd ├── summary.Metaboprep.Rd ├── total_peak_area.Rd ├── tree_and_independent_features.Rd └── variable_by_factor.Rd ├── metaboprep.Rproj ├── pkgdown └── favicon │ ├── apple-touch-icon.png │ ├── favicon-96x96.png │ ├── favicon.ico │ ├── favicon.svg │ ├── site.webmanifest │ ├── web-app-manifest-192x192.png │ └── web-app-manifest-512x512.png ├── scripts └── DEVELOPMENT_AREA.R ├── tests ├── testthat.R └── testthat │ ├── test-metaboprep1.R │ ├── test-missingness.R │ └── test-sample_pca_outlier.R └── vignettes ├── .gitignore ├── batch_normalise.Rmd ├── export.Rmd ├── feature_summary.Rmd ├── generate_report.Rmd ├── metabolon.Rmd ├── nightingale.Rmd ├── olink.Rmd ├── quality_control.Rmd ├── sample_summary.Rmd └── somalogic.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MRCIEU/metaboprep/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MRCIEU/metaboprep/HEAD/.github/workflows/pkgdown.yaml -------------------------------------------------------------------------------- /.gitignore: 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