MetaboReport

Shiny app for metabolomics data preprocessing, statistical analysis, visualisation, and self-contained HTML reporting.

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News 👀

Updated on 2026.07.31

Release of v0.3.6

• User manual updated
• Logo updated
• Faster in data analysis
• Bug fixed in report generation
• Report content generated
• Allow to generate Chinese report

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Installation

You can use one of the following ways to use and install MetaboReport.

(a) Install as a standalone App

Note This is the easiest way to install and use MetaboReport (recommended)

Download

(b) Inatall as an R package

remotes::install_github("YonghuiDong/MetaboReport")

Note After installation, you can use library(MetaboReport); run_app() or MetaboReport::run_app() to start the app.

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Project structure

• R/app_*.R contains application configuration, shared state, UI, and server composition.
• R/mod_*.R contains Shiny modules. Modules communicate through the state object created by new_app_state().
• R/fct_*.R contains pure analysis, input/output, plotting, and report functions.
• R/ui_components.R contains reusable UI elements.
• inst/app/www/ contains packaged web and report resources.
• tests/testthat/ contains automated regression tests.
• dev/ contains development and deployment helpers and is excluded from the built package.

The supported public package API is intentionally small: run_app(). Analysis helpers are internal so their implementation can evolve without creating an accidental compatibility contract.

Development checks

roxygen2::roxygenise()
testthat::test_local()
rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes"))

Citation

Dong, Y. and Malitsky, S., 2024. MetaboReport: from metabolomics data analysis to comprehensive reporting. Bioinformatics, 40(6), p.btae373. DOI: 10.1093/bioinformatics/btae373