Updated readme

MannLabs · Mar 11, 2024 · 406f118 · 406f118
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diff --git a/README.md b/README.md
@@ -3,38 +3,30 @@ AlphaPept
 
 <!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
 
-![CI](https://github.com/MannLabs/alphapept/workflows/CI/badge.svg)
-![Quick
-Test](https://github.com/MannLabs/alphapept/workflows/Quick%20Test/badge.svg)
-![Performance
-test](https://github.com/MannLabs/alphapept/actions/workflows/performance_test_installer.yml/badge.svg)
-![Windows
-Installer](https://github.com/MannLabs/alphapept/workflows/Windows%20Installer/badge.svg)
+[![nbdev
+CI](https://github.com/MannLabs/alphapept/actions/workflows/nbdev.yaml/badge.svg?branch=master)](https://github.com/MannLabs/alphapept/actions/workflows/nbdev.yaml)
 [![launch -
 renku](https://renkulab.io/renku-badge.svg)](https://renkulab.io/projects/renku-stories/alphapept-gui-streamlit)
+[![DOI:10.1038/s41467-024-46485-4](http://img.shields.io/badge/DOI-10.1038/s41467-024-46485-4-B31B1B.svg)](https://doi.org/10.1038/s41467-024-46485-4)
 
-<div>
+![](https://i.imgur.com/xkFtDff.jpg)
 
-[![](http://img.shields.io/badge/DOI-10.1101/2021.07.23.453379-B31B1B.svg)](https://www.biorxiv.org/content/10.1101/2021.07.23.453379v1)
+**AlphaPept: a modern and open framework for MS-based proteomics**
 
-DOI:10.1101/2021.07.23.453379
+[Nature Communications](https://doi.org/10.1038/s41467-024-46485-4).
 
-</div>
+Be sure to check out other packages of our ecosystem:
 
-## Preprint
-
-Our preprint **AlphaPept, a modern and open framework for MS-based
-proteomics** is now available
-[here.](https://www.biorxiv.org/content/10.1101/2021.07.23.453379v1)
-
-Be sure to check out other packages of our ecosystem: -
-[alphatims](https://github.com/MannLabs/alphatims): Fast access to
-TimsTOF data. - [alphamap](https://github.com/MannLabs/alphamap):
-Peptide level MS data exploration. -
-[alphapeptdeep](https://github.com/MannLabs/alphapeptdeep): Predicting
-properties from peptides. -
-[alphaviz](https://github.com/MannLabs/alphaviz): Vizualization of MS
-data.
+- [alphatims](https://github.com/MannLabs/alphatims): Fast access to
+  TimsTOF data.
+- [alphamap](https://github.com/MannLabs/alphamap): Peptide level MS
+  data exploration.
+- [alphapeptdeep](https://github.com/MannLabs/alphapeptdeep): Predicting
+  properties from peptides.
+- [alphapeptstats](https://github.com/MannLabs/alphapeptstats):
+  Downstream analysis of MS data
+- [alphaviz](https://github.com/MannLabs/alphaviz): Vizualization of MS
+  data.
 
 ## Windows Quickstart
 
@@ -400,14 +392,8 @@ If you like the project, consider starring it!
 
 ## Cite us
 
-    @article {Strauss2021.07.23.453379,
-        author = {Strauss, Maximilian T and Bludau, Isabell and Zeng, Wen-Feng and Voytik, Eugenia and Ammar, Constantin and Schessner, Julia and Ilango, Rajesh and Gill, Michelle and Meier, Florian and Willems, Sander and Mann, Matthias},
-        title = {AlphaPept, a modern and open framework for MS-based proteomics},
-        elocation-id = {2021.07.23.453379},
-        year = {2021},
-        doi = {10.1101/2021.07.23.453379},
-        publisher = {Cold Spring Harbor Laboratory},
-        URL = {https://www.biorxiv.org/content/early/2021/07/26/2021.07.23.453379},
-        eprint = {https://www.biorxiv.org/content/early/2021/07/26/2021.07.23.453379.full.pdf},
-        journal = {bioRxiv}
-    }
+If you use this project in your research, please cite:
+
+> Strauss, M.T., Bludau, I., Zeng, WF. et al. AlphaPept: a modern and
+> open framework for MS-based proteomics. Nat Commun 15, 2168 (2024).
+> https://doi.org/10.1038/s41467-024-46485-4
diff --git a/nbs/index.ipynb b/nbs/index.ipynb
@@ -4,39 +4,45 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "![CI](https://github.com/MannLabs/alphapept/workflows/CI/badge.svg)\n",
-    "![Quick Test](https://github.com/MannLabs/alphapept/workflows/Quick%20Test/badge.svg)\n",
-    "![Performance test](https://github.com/MannLabs/alphapept/actions/workflows/performance_test_installer.yml/badge.svg)\n",
-    "![Windows Installer](https://github.com/MannLabs/alphapept/workflows/Windows%20Installer/badge.svg)\n",
-    "[![launch - renku](https://renkulab.io/renku-badge.svg)](https://renkulab.io/projects/renku-stories/alphapept-gui-streamlit)\n",
     "\n",
-    "[![DOI:10.1101/2021.07.23.453379](http://img.shields.io/badge/DOI-10.1101/2021.07.23.453379-B31B1B.svg)](https://www.biorxiv.org/content/10.1101/2021.07.23.453379v1)"
+    "[![nbdev CI](https://github.com/MannLabs/alphapept/actions/workflows/nbdev.yaml/badge.svg?branch=master)](https://github.com/MannLabs/alphapept/actions/workflows/nbdev.yaml)\n",
+    "[![launch - renku](https://renkulab.io/renku-badge.svg)](https://renkulab.io/projects/renku-stories/alphapept-gui-streamlit)\n",
+    "[![DOI:10.1038/s41467-024-46485-4](http://img.shields.io/badge/DOI-10.1038/s41467-024-46485-4-B31B1B.svg)](https://doi.org/10.1038/s41467-024-46485-4)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# AlphaPept\n",
-    "![](https://i.imgur.com/xkFtDff.jpg)\n",
-    " > A modular, python-based framework to analyze mass spectrometry data. Powered by nbdev. Supercharged with numba."
+    "# AlphaPept"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Preprint\n",
+    "![](https://i.imgur.com/xkFtDff.jpg)\n",
     "\n",
-    "Our preprint **AlphaPept, a modern and open framework for MS-based proteomics** is now available [here.](https://www.biorxiv.org/content/10.1101/2021.07.23.453379v1)\n",
+    "**AlphaPept: a modern and open framework for MS-based proteomics**\n",
+    "\n",
+    "[Nature Communications](https://doi.org/10.1038/s41467-024-46485-4).\n",
     "\n",
     "Be sure to check out other packages of our ecosystem:\n",
+    "\n",
     "- [alphatims](https://github.com/MannLabs/alphatims): Fast access to TimsTOF data.\n",
     "- [alphamap](https://github.com/MannLabs/alphamap): Peptide level MS data exploration.\n",
     "- [alphapeptdeep](https://github.com/MannLabs/alphapeptdeep): Predicting properties from peptides.\n",
+    "- [alphapeptstats](https://github.com/MannLabs/alphapeptstats): Downstream analysis of MS data\n",
     "- [alphaviz](https://github.com/MannLabs/alphaviz): Vizualization of MS data."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -333,19 +339,9 @@
    "source": [
     "## Cite us\n",
     "\n",
-    "```\n",
-    "@article {Strauss2021.07.23.453379,\n",
-    "\tauthor = {Strauss, Maximilian T and Bludau, Isabell and Zeng, Wen-Feng and Voytik, Eugenia and Ammar, Constantin and Schessner, Julia and Ilango, Rajesh and Gill, Michelle and Meier, Florian and Willems, Sander and Mann, Matthias},\n",
-    "\ttitle = {AlphaPept, a modern and open framework for MS-based proteomics},\n",
-    "\telocation-id = {2021.07.23.453379},\n",
-    "\tyear = {2021},\n",
-    "\tdoi = {10.1101/2021.07.23.453379},\n",
-    "\tpublisher = {Cold Spring Harbor Laboratory},\n",
-    "\tURL = {https://www.biorxiv.org/content/early/2021/07/26/2021.07.23.453379},\n",
-    "\teprint = {https://www.biorxiv.org/content/early/2021/07/26/2021.07.23.453379.full.pdf},\n",
-    "\tjournal = {bioRxiv}\n",
-    "}\n",
-    "```"
+    "If you use this project in your research, please cite:\n",
+    "\n",
+    "> Strauss, M.T., Bludau, I., Zeng, WF. et al. AlphaPept: a modern and open framework for MS-based proteomics. Nat Commun 15, 2168 (2024). https://doi.org/10.1038/s41467-024-46485-4"
    ]
   },
   {