---
title: "MRMhub"
author: "Bo Burla"
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_vignette:
    toc: true
    toc_depth: 3
    fig_width: 6
    fig_height: 4
vignette: >
  %\VignetteIndexEntry{MRMhub}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  markdown: 
    wrap: 72
---

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```{r pkgs, include=FALSE}
library(mrmhub)
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  comment = "#>",
  root.dir = tempdir()
)
```

## Overview

MRMhub is a set of tools for reproducible raw data processing, post-processing, quality control, and reporting of targeted quantitative small-molecule mass spectrometry experiments using Multiple Reaction Monitoring (MRM). The platform includes two complementary tools:

-   **INTEGRATOR**: standalone application for automated peak detection, picking, and integration from mzML files.

-   **QUANT**: R package providing a function library for data post- processing, including quantitation, data corrections, quality control, and reporting.

The modular functionalities and defined data structures support diverse analytical designs, data formats, and processing tasks, as found in metabolomics, lipidomics and other quantitative small molecule analyses. `MRMhub` is intended for both analytical and bioinformatics scientists and supports collaboration between them. It enables the creation of efficient, customizable, supervisable, and documented end-to-end data processing workflows through its functions and data objects.

## Usage

#### INTEGRATOR (Peak Integration)

To download the latest release of INTEGRATOR, visit the [Releases page](https://github.com/SLINGhub/MRMhub/releases). Choose the appropriate version for your operating system (Windows, macOS, or Linux) and download the corresponding executable file. Unzip the downloaded file and double-click the executable to launch the application. Refer to the [Documentation](https://slinghub.github.io/MRMhub/integrator/) for detailed instructions on how to use INTEGRATOR.

#### QUANT (Postprocessing and Quality Control)

Read the [Installation guide](https://slinghub.github.io/MRMhub/quant/articles/manual-00-installation.html) before installing the `mrmhub` package.

``` r
# mrmhub from the MRMhub R-universe repository, dependencies from CRAN
install.packages("mrmhub",
                 repos = c("https://slinghub.r-universe.dev",
                           "https://cloud.r-project.org"))
library(mrmhub)
```

Installation from GitHub with `pak` or `remotes` is described in that guide. For detailed usage instructions and examples, refer to the [Documentation](https://slinghub.github.io/MRMhub/quant/).

## Documentation

See the online Documentation on [https://slinghub.github.io/MRMhub/quant/](https://slinghub.github.io/MRMhub/quant/) for detailed information on installation, usage, and examples of MRMhub.

## Contributing

We welcome contributions. For questions, bug reports, feature requests, or suggestions, please contact us directly or submit an issue through the [GitHub issues](https://github.com/SLINGhub/MRMhub/issues) page.

## Contributor Code of Conduct

Please note that the MRMhub project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## Dual Licensing Options
The source code and models within this repository are dual licenced. You may choose to use it under the terms of the [GNU AGPLv3](https://www.gnu.org/licenses/agpl-3.0.en.html) for non-commercial purposes, or you can obtain a commercial license for commercial use.

For non-commercial uses and licensing of this / these code and models and its derivatives, an open-source licence is granted in accordance with the following terms and conditions -
[GNU AGPLv3](https://www.gnu.org/licenses/agpl-3.0.en.html).
### For commercial use and licensing of this / these code and models, please contact -
 Jonathan Tan ( jonathan_tan@nus.edu.sg )


Reporting unauthorized commercial use and/or further enquiries

If you become aware of any unauthorised commercial use of this source code and models or have any questions regarding licensing terms, please contact Jonathan Tan ( jonathan_tan@nus.edu.sg ).

## Next Steps

- [Installation](https://slinghub.github.io/MRMhub/quant/articles/manual-00-installation.html) - requirements and setup
- [MRMhub overview](https://slinghub.github.io/MRMhub/quant/articles/manual-01-key-concepts.html) - core terminology and the MRMhubExperiment object
- [Getting started with MRMhub](https://slinghub.github.io/MRMhub/quant/articles/tutorial-02-getting-started-mrmhub.html) - a short end-to-end walkthrough