add citation and link to manuscript

MannLabs · Jun 2, 2023 · 29168a3 · 29168a3
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diff --git a/README.md b/README.md
@@ -1,10 +1,9 @@
-[![Python package](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml/badge.svg?branch=release)](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml) [![Python package](https://img.shields.io/badge/version-v1.0.0-blue)](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml) [![Python package](https://img.shields.io/badge/license-MIT-blue)](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml)
+[![Python package](https://img.shields.io/badge/version-v1.0.0-blue)](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml) [![Python package](https://img.shields.io/badge/license-MIT-blue)](https://github.com/MannLabs/SPARCSpy/actions/workflows/python-package.yml)
 [![website](https://img.shields.io/website?url=https%3A%2F%2Fmannlabs.github.io/SPARCSpy/html/index.html)](https://mannlabs.github.io/SPARCSpy/html/index.html)
 
 SPARCSpy is a scalable toolkit to analyse SPARCS datasets. The python implementation efficiently segments individual cells, generates single-cell datasets and provides tools for the efficient deep learning classification of their phenotypes and subsequent excision using Laser Microdissection.
 
-Installation from Github
-========================
+## Installation from Github
 
 SPARCSpy has been tested with **Python 3.8 and 3.9**.
 To install the SPARCSpy library clone the Github repository and use pip to install the library in your current environment. It is recommended to use the library with a conda environment. Please make sure that the package is installed editable like described. Otherwise pretrained models might not be available.
@@ -50,6 +49,14 @@ Once these steps are completed you can proceed to install the SPARCSpy package v
 pip install -e .
 ```
 
-Documentation
-==============
+## Documentation
+
 The current documentation can be found under https://mannlabs.github.io/SPARCSpy/html/index.html.
+
+## Citing our Work
+
+py-lmd was developed by Georg Wallmann, Sophia Mädler and Niklas Schmacke in the labs of Veit Hornung and Matthias Mann. If you use our code please cite the [following manuscript](https://www.biorxiv.org/content/10.1101/2023.06.01.542416v1):
+
+SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes
+Niklas Arndt Schmacke, Sophia Clara Maedler, Georg Wallmann, Andreas Metousis, Marleen Berouti, Hartmann Harz, Heinrich Leonhardt, Matthias Mann, Veit Hornung
+bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/...otebooks/example_sparcspy_project 2.ipynb → ...otebooks/example_sparcspy_project 3.ipynb b/...otebooks/example_sparcspy_project 2.ipynb → ...otebooks/example_sparcspy_project 3.ipynb
diff --git a/docs/doctrees/pages/ecosystem 2.doctree b/docs/doctrees/pages/ecosystem 2.doctree
diff --git a/docs/doctrees/pages/ecosystem/installation 2.doctree b/docs/doctrees/pages/ecosystem/installation 2.doctree
diff --git a/docs/doctrees/pages/guides/basic_workflow 2.doctree b/docs/doctrees/pages/guides/basic_workflow 2.doctree
diff --git a/docs/doctrees/pages/module/ml 2.doctree b/docs/doctrees/pages/module/ml 2.doctree
diff --git a/docs/doctrees/pages/notebooks/example_sparcspy_project 2.doctree b/docs/doctrees/pages/notebooks/example_sparcspy_project 2.doctree
diff --git a/docs/doctrees/pages/pipeline/classification 2.doctree b/docs/doctrees/pages/pipeline/classification 2.doctree
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
@@ -11,9 +11,12 @@ Check the installation instructions :ref:`here<installation>`.
 Citing our Work
 ================
 
-SPARCSpy was developed by Sophia Mädler, Georg Wallmann and Niklas Schmacke in the labs of Matthias Mann and Veit Hornung. If you use our code please cite the following manuscript:
+SPARCSpy was developed by Sophia Mädler, Georg Wallmann and Niklas Schmacke in the labs of Matthias Mann and Veit Hornung. 
+If you use our code please cite the `following manuscript <https://doi.org/10.1101/2023.06.01.542416>`_:
 
-CITATION HERE
+SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes
+Niklas Arndt Schmacke, Sophia Clara Maedler, Georg Wallmann, Andreas Metousis, Marleen Berouti, Hartmann Harz, Heinrich Leonhardt, Matthias Mann, Veit Hornung
+bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/html/_sources/pages/ecosystem.rst 2.txt b/docs/html/_sources/pages/ecosystem.rst 2.txt
diff --git a/docs/html/_sources/pages/ecosystem/installation.rst 2.txt b/docs/html/_sources/pages/ecosystem/installation.rst 2.txt
diff --git a/docs/html/_sources/pages/guides/basic_workflow.rst 2.txt b/docs/html/_sources/pages/guides/basic_workflow.rst 2.txt
diff --git a/docs/html/_sources/pages/module.rst 2.txt b/docs/html/_sources/pages/module.rst 2.txt
diff --git a/docs/html/_sources/pages/module/ml.rst 2.txt b/docs/html/_sources/pages/module/ml.rst 2.txt
diff --git a/docs/html/_sources/pages/module/pipeline.rst 2.txt b/docs/html/_sources/pages/module/pipeline.rst 2.txt
diff --git a/docs/html/_sources/pages/module/processing.rst 2.txt b/docs/html/_sources/pages/module/processing.rst 2.txt