diff --git a/README.md b/README.md index 99f2f14..29d45e7 100644 --- a/README.md +++ b/README.md @@ -2,55 +2,42 @@ Data-Driven Optimization of Mass Spectrometry 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) - + ## 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 - +![](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. - +![](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. @@ -59,9 +46,9 @@ DO-MS is designed to be easily user-customizable for in-house proteomics workflo 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... ? @@ -71,13 +58,8 @@ While the base library of modules are based around bottom-up proteomics by LC-MS ## About the 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). @@ -87,21 +69,11 @@ DO-MS is distributed by an [MIT license](https://github.com/SlavovLab/DO-MS/blob ### Contributing -Please feel free to contribute to this project by opening an issue or pull request. - - - - +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. diff --git a/docs/index.md b/docs/index.md index 68ff4de..d2f82e2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -33,7 +33,8 @@ Install this application by downloading it from the [release page](https://githu ## 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