Add data and notebooks

Co-authored-by: Laura Helleckes <[email protected]>

Author: michaelosthege

README.md

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+This repository contains the raw data and analysis that are the supporting information to the [`calibr8`](https://github.com/jubiotech/calibr8) paper.
+
+# Contents
+The material is organized by the chapter of first appearance in the manuscript.
+The `raw_data` directory contains unprocessed result files.
+
+# Installation
+A Python environment for running the notebooks can be created with the following command:
+
+```
+conda env create -f environment.yml
+```
+
+The new environment is named `murefi_env` and can be activated with `conda activate murefi_env`.
+
+After that a Jupyter notebook server can be launched with `jupyter notebook`.
+
+Note: The only notebook not executable is `00_Preprocessing.ipynb`.
+This notebook relies on unpublished software. 
+However, all processed data is included as XLSX or HDF5 files in the `processed` directory and the data analysis can be re-run accordingly.
+
+# References
+* [Preprint on bioRxiv](https://doi.org/10.1101/2021.06.30.450546)
+* [`calibr8` source code](https://github.com/JuBiotech/calibr8)
+* [`calibr8` documentation](https://calibr8.readthedocs.io)
+* [`murefi` source code](https://github.com/JuBiotech/murefi)
+* [`murefi` documentation](https://murefi.readthedocs.io)