diff --git a/README.md b/README.md index f596c54f..2e755051 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ - +MS²Rescore

[![GitHub release](https://img.shields.io/github/release-pre/compomics/ms2rescore.svg?style=flat-square)](https://github.com/compomics/ms2rescore/releases) @@ -10,6 +10,10 @@ Modular and user-friendly platform for AI-assisted rescoring of peptide identifications +> ⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore, which is +> now in the beta stage. While MS²Rescore 3.0 has been drastically improved over the previous +> version, you might run into some unforeseen issues. Please report any issues you encounter on the +> [issue tracker][issues] or post your questions on the [GitHub Discussions][discussions] forum. ## About MS²Rescore @@ -23,17 +27,18 @@ such as proteogenomics, metaproteomics, or immunopeptidomics. MS²Rescore can read peptide identifications in any format supported by [psm_utils][psm_utils] (see [Supported file formats][file-formats]) and has been tested with various search engines output -files ( -[PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) `.mzid`, -[MaxQuant](https://www.maxquant.org/) `msms.txt`, -[MSGFPlus](https://omics.pnl.gov/software/ms-gf) `.mzid`, -[X!Tandem](https://www.thegpm.org/tandem/) X!Tandem `.xml`, and -[PEAKS](https://www.bioinfor.com/peaksdb/) `.mzid`). +files: + +- [MS Amanda](http://ms.imp.ac.at/?goto=msamanda) `.csv` +- [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) `.mzid` +- [MSGFPlus](https://omics.pnl.gov/software/ms-gf) `.mzid` +- [MaxQuant](https://www.maxquant.org/) `msms.txt` +- [X!Tandem](https://www.thegpm.org/tandem/) X!Tandem `.xml` +- [PEAKS](https://www.bioinfor.com/peaksdb/) `.mzid` MS²Rescore is available as a [desktop application][desktop], a [command line tool][cli], and a [modular Python API][python-package]. - ## Citing **Latest MS²Rescore publication:** @@ -41,38 +46,34 @@ MS²Rescore is available as a [desktop application][desktop], a [command line to > **MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates.** > Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, and Ralf Gabriels. > _Molecular & Cellular Proteomics_ (2021) [doi:10.1016/j.mcpro.2022.100266](https://doi.org/10.1016/j.mcpro.2022.100266) -> +> **Original publication describing the concept of rescoring with predicted spectra:** > **Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions.** > Ana S C Silva, Robbin Bouwmeester, Lennart Martens, and Sven Degroeve. > _Bioinformatics_ (2019) [doi:10.1093/bioinformatics/btz383](https://doi.org/10.1093/bioinformatics/btz383) -> +> To replicate the experiments described in this article, check out the [publication branch][publication-branch] of the repository. - ## Getting started The desktop application can be installed on Windows with a [one-click installer][desktop-installer]. The Python package and command line interface can be installed with `pip`, `conda`, or `docker`. Check out the [full documentation][docs] to get started. - ## Questions or issues? Have questions on how to apply MS²Rescore on your data? Or ran into issues while using MS²Rescore? Post your questions on the [GitHub Discussions][discussions] forum and we are happy to help! - ## How to contribute Bugs, questions or suggestions? Feel free to post an issue in the [issue tracker][issues] or to make a [pull request][pr]! - [docs]: https://ms2rescore.readthedocs.io/ [issues]: https://github.com/compomics/ms2rescore/issues/ [discussions]: https://github.com/compomics/ms2rescore/discussions/ diff --git a/docs/source/_static/js/badge.min.js b/docs/source/_static/js/badge.min.js new file mode 100644 index 00000000..3981d00d --- /dev/null +++ b/docs/source/_static/js/badge.min.js @@ -0,0 +1 @@ +(()=>{var t={7633(t,e,r){r(9170),r(6992),r(1539),r(8674),r(7922),r(4668),r(7727),r(8783);var n=r(857);t.exports=n.Promise},9662(t,e,r){var n=r(7854),o=r(614),i=r(6330),a=n.TypeError;t.exports=function(t){if(o(t))return t;throw a(i(t)+" is not a function")}},9483(t,e,r){var n=r(7854),o=r(4411),i=r(6330),a=n.TypeError;t.exports=function(t){if(o(t))return t;throw a(i(t)+" is not a constructor")}},6077(t,e,r){var n=r(7854),o=r(614),i=n.String,a=n.TypeError;t.exports=function(t){if("object"==typeof t||o(t))return t;throw a("Can't set 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