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updated README
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GeorgWa committed Mar 1, 2023
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58 changes: 15 additions & 43 deletions README.md
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<u>D</u>ata-Driven <u>O</u>ptimization of <u>M</u>ass <u>S</u>pectrometry Methods

![Python Package](https://github.com/SlavovLab/DO-MS-DIA/actions/workflows/python-package.yml/badge.svg)
![GitHub release](https://img.shields.io/github/release/SlavovLab/DO-MS.svg)
![GitHub](https://img.shields.io/github/license/SlavovLab/DO-MS.svg)

* [Website](https://do-ms.slavovlab.net)
* [Get started now](#getting-started)
* [Download](https://github.com/SlavovLab/DO-MS/releases/latest)
* [Manuscript](https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00039)
* [BioArxiv Preprint](https://www.biorxiv.org/content/10.1101/2023.02.02.526809v1)

<img src="https://do-ms.slavovlab.net/assets/images/TOC_Graphic_noOutline_abstract_v18.png" width="70%">
<img src="https://do-ms.slavovlab.net/assets/images/do-ms-dia_title_v2.png" width="70%">


## Getting Started

Please read our detailed getting started guides:
* [Getting started on the application](https://do-ms.slavovlab.net/docs/getting-started-application)
* [Getting started on the command-line](https://do-ms.slavovlab.net/docs/getting-started-command-line)
* [Getting started with DIA preprocessing](https://do-ms.slavovlab.net/docs/getting-started-preprocessing)
* [Getting started with DIA reports](https://do-ms.slavovlab.net/docs/getting-started-dia-app)
* [Getting started with DDA reports](https://do-ms.slavovlab.net/docs/getting-started-dda-app)

### Requirements

This application has been tested on R >= 4.0.0 and R <= 4.0.2, OSX 10.14 / Windows 7/8/10. R can be downloaded from the main [R Project page](https://www.r-project.org/) or downloaded with the [RStudio Application](https://www.rstudio.com/products/rstudio/download/). All modules are maintained for MaxQuant >= 1.6.0.16 and MaxQuant < 2.0
This application has been tested on R >= 3.5.0, OSX 10.14 / Windows 7/8/10/11. R can be downloaded from the main [R Project page](https://www.r-project.org/) or downloaded with the [RStudio Application](https://www.rstudio.com/products/rstudio/download/). All modules are maintained for MaxQuant >= 1.6.0.16 and DIA-NN > 1.8.1.

The application suffers from visual glitches when displayed on unsupported older browsers (such as IE9 commonly packaged with RStudio on Windows). Please use IE >= 11, Firefox, or Chrome for the best user experience.

### Installation

Install this application by downloading it from the [release page](https://github.com/SlavovLab/DO-MS/releases/latest).

### Running
### Running the Interactive Application

The easiest way to run the app is directly through RStudio, by opening the `DO-MS.Rproj` Rproject file

<img src="https://github.com/SlavovLab/DO-MS/raw/master/docs/assets/images/do-ms-proj.png" height="100px">
![](https://do-ms.slavovlab.net/assets/images/do-ms-proj.png){: width="70%" .center-image}

and clicking the "Run App" button at the top of the application, after opening the `server.R` file. We recommend checking the "Run External" option to open the application in your default browser instead of the RStudio Viewer.

<img src="https://github.com/SlavovLab/DO-MS/raw/master/docs/assets/images/do-ms-run.png" height="100px">
![](https://do-ms.slavovlab.net/assets/images/do-ms-run.png){: width="70%" .center-image}

You can also start the application by running the `start_server.R` script.

### Automated Report Generation

You can automatically generate PDF/HTML reports without having to launch the server by running the `do-ms_cmd.R` script, like so:

```
$ Rscript do-ms_cmd.R config_file.yaml
```

This requires a configuration file, and you can [find an example one here](https://github.com/SlavovLab/DO-MS/blob/master/example/config_file.yaml). See [Automating Report Generation](https://do-ms.slavovlab.net/docs/automation) for more details and instructions.

### Customization

DO-MS is designed to be easily user-customizable for in-house proteomics workflows. Please see [Building Your Own Modules](https://do-ms.slavovlab.net/docs/build-your-own) for more details.
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Please see [Hosting as a Server](https://do-ms.slavovlab.net/docs/hosting-as-server) for more details.

### Search Engines Other Than MaxQuant
### Supporting other Search Engines

This application is currently maintained for MaxQuant >= 1.6.0.16. Adapting to other search engines is possible but not provided out-of-the-box. Please see [Integrating Other Search Engines ](https://do-ms.slavovlab.net/docs/other-search-engines) for more details.
This application is currently maintained for (MaxQuant)[https://www.nature.com/articles/nbt.1511] >= 1.6.0.16 and (DIA-NN)[https://www.nature.com/articles/s41592-019-0638-x] >= 1.8. Adapting to other search engines is possible but not provided out-of-the-box. Please see [Integrating Other Search Engines ](https://do-ms.slavovlab.net/docs/other-search-engines) for more details.

### Can I use this for Metabolomics, Lipidomics, etc... ?

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## About the project

<!--
DO-MS is a project...
-->

The manuscript for this tool is published at the Journal of Proteome Research: [https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00039](https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00039)

The manuscript is also freely available on bioRxiv: [https://www.biorxiv.org/content/10.1101/512152v1](https://www.biorxiv.org/content/10.1101/512152v1).
The manuscript for the extended version 2.0 can be found on bioArxiv: [https://www.biorxiv.org/content/10.1101/2023.02.02.526809v1](https://www.biorxiv.org/content/10.1101/2023.02.02.526809v1)

Contact the authors by email: [nslavov\{at\}northeastern.edu](mailto:nslavov@northeastern.edu).

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### Contributing

Please feel free to contribute to this project by opening an issue or pull request.

<!--
### Data
All data used for the manuscript is available on [UCSD's MassIVE Repository](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ed5a1ab37dc34985bbedbf3d9a945535)
-->

<!--
### Figures/Analysis
Scripts for the figures in the DART-ID manuscript are available in a separate GitHub repository, [https://github.com/SlavovLab/DART-ID_2018](https://github.com/SlavovLab/DART-ID_2018)
-->
Please feel free to contribute to this project by opening an issue or pull request in the [GitHub repository](https://github.com/SlavovLab/DO-MS).

-------------

## Help!

For any bugs, questions, or feature requests,
For any bugs, questions, or feature requests,
please use the [GitHub issue system](https://github.com/SlavovLab/DO-MS/issues) to contact the developers.
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## Getting Started
Please read our detailed getting started guides:
* [Getting started with DIA preprocessing]({{site.baseurl}}/docs/getting-started-preprocessing)
* [Getting started on the application]({{site.baseurl}}/docs/getting-started-application)
* [Getting started with DIA reports]({{site.baseurl}}/docs/getting-started-dia-app)
* [Getting started with DDA reports]({{site.baseurl}}/docs/getting-started-dda-app)


### Requirements
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