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docs/example_data/Basic_example_vuegen_demo_notebook/5_Markdown/1_All_markdown/README.md

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<!-- <div align="center">
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<img width="300px" src="images/vuegen_logo.svg">
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</div> -->
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![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg)
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-----------------
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![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.png)
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<p align="center">
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VueGen is a Python library that automates the creation of scientific reports.
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</p>
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| Information | Links |
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| :--- | :--- |
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| **Package** |[ ![PyPI Latest Release](https://img.shields.io/pypi/v/vuegen.svg)](https://pypi.org/project/vuegen/) [![Supported versions](https://img.shields.io/pypi/pyversions/vuegen.svg)](https://pypi.org/project/vuegen/)|
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| **Documentation** | [![Docs](https://readthedocs.org/projects/vuegen/badge/?style=flat)](https://vuegen.readthedocs.io/)|
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| **Build** | [![CI](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml/badge.svg)](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml) [![Docs](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml/badge.svg)](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml)|
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| **Examples** | [![HTML5](https://img.shields.io/badge/html5-%23E34F26.svg?style=for-the-badge&logo=html5&logoColor=white)](https://multiomics-analytics-group.github.io/vuegen/) [![Streamlit](https://img.shields.io/badge/Streamlit-%23FE4B4B.svg?style=for-the-badge&logo=streamlit&logoColor=white)](https://multiomics-analytics-group.github.io/vuegen/)|
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| **Discuss on GitHub** | [![GitHub issues](https://img.shields.io/github/issues/Multiomics-Analytics-Group/vuegen)](https://github.com/Multiomics-Analytics-Group/vuegen/issues) [![GitHub pull requests](https://img.shields.io/github/issues-pr/Multiomics-Analytics-Group/vuegen)](https://github.com/Multiomics-Analytics-Group/vuegen/pulls) |
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| Information | Links |
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| :-------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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| **Package** | [PyPI Latest Release](https://pypi.org/project/vuegen/) [Supported versions](https://pypi.org/project/vuegen/) |
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| **Documentation** | [Docs](https://vuegen.readthedocs.io/) |
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| **Build** | [CI](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml) - [Docs](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml) |
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| **Examples** | [HTML5](https://multiomics-analytics-group.github.io/vuegen/) - [Streamlit](https://multiomics-analytics-group.github.io/vuegen/) |
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| **Discuss on GitHub** | [GitHub issues](https://github.com/Multiomics-Analytics-Group/vuegen/issues) - [GitHub pull requests](https://github.com/Multiomics-Analytics-Group/vuegen/pulls) |
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## Table of contents:
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- [About the project](#about-the-project)
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- [Installation](#installation)
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- [Execution](#execution)
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- [Acknowledgements](#acknowledgements)
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- [Contact](#contact)
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## About the project
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VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input.
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VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input.
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The configuration file specifies the structure of the report, including sections, subsections, and various components such as plots, dataframes, markdown, html, and API calls. Reports can be generated in various formats, including documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), notebooks (Jupyter) or [Streamlit](streamlit) web applications.
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<img width="650px" src="images/vuegen_graph_abstract.png" alt="VueGen overview"/>
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</figure>
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</p> -->
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![VueGen Abstract](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png)
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Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes:
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You can also install the package for development from this repository by running the following command:
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```bash
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pip install -e path/to/vuegen # specify location
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pip install -e path/to/vuegen # specify location
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pip install -e . # in case your pwd is in the vuegen directory
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```
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```
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The current report types supported by VueGen are:
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* Streamlit
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* HTML
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* PDF
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* DOCX
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* ODT
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* Reveal.js
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* PPTX
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* Jupyter
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- Streamlit
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- HTML
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- PDF
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- DOCX
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- ODT
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- Reveal.js
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- PPTX
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- Jupyter
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## Acknowledgements
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- Vuegen was developed by the [Multiomics Network Analytics Group (MoNA)][Mona] at the [Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)][Biosustain].
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- The vuegen logo was designed based on an image created by [Scriberia][scriberia] for The [Turing Way Community][turingway], which is shared under a CC-BY licence. The original image can be found at [Zenodo][zenodo-turingway].
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## Contact
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If you have comments or suggestions about this project, you can [open an issue][issues] in this repository.
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[streamlit]: https://streamlit.io/
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[streamlit]: https://streamlit.io/
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[vuegen-pypi]: https://pypi.org/project/vuegen/
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[quarto]: https://quarto.org/
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[quarto-cli-pypi]: https://pypi.org/project/quarto-cli/
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[turingway]: https://github.com/the-turing-way/the-turing-way
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[zenodo-turingway]: https://zenodo.org/records/3695300
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[issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
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