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| Information | Links |
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|**Package**|[][vuegen-pypi][][vuegen-pypi][![Docker Repository on Quay](https://quay.io/repository/dtu_biosustain_dsp/vuegen/status"Docker Repository on Quay")][vuegen-docker-quay]|
-[Credits and acknowledgements](#credits-and-acknowledgements)
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-[Citation](#citation)
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-[Contact and feedback](#contact-and-feedback)
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## About the project
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The VueGen documentation is available at [vuegen.readthedocs.io][vuegen-docs], where you can find detailed information of the package’s classes and functions, installation and execution instructions, and case studies to demonstrate its functionality.
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## Installation
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Vuegen is available on [PyPI][vuegen-pypi] and can be installed using pip:
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### Pip
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VueGen is available on [PyPI][vuegen-pypi] and can be installed using pip:
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```bash
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pip install vuegen
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```
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You can also install the package for development from this repository by running the following command:
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You can also install the package for development by cloning this repository and 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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> [!TIP]
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> It is recommended to install VueGen inside a virtual environment to manage depenendencies and avoid conflicts with existing packages. You can use the virtual environment manager of your choice, such as `poetry`, `conda`, or `pipenv`.
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Vuegen uses [Quarto][quarto] to generate various report types. The pip insallation includes quarto using the [quarto-cli Python library][quarto-cli-pypi]. To test if quarto is installed in your computer, run the following command:
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### Conda
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VueGen is also available on [Bioconda][vuegen-conda] and can be installed using conda:
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```bash
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conda install bioconda::vuegen
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```
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### Dependencies
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VueGen uses [Quarto][quarto] to generate various report types. The pip insallation includes quarto using the [quarto-cli Python library][quarto-cli-pypi]. To test if quarto is installed in your computer, run the following command:
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```bash
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quarto check
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> [!TIP]
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> If quarto is not installed, you can download the command-line interface from the [Quarto website][quarto-cli] for your operating system.
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### Docker
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If you prefer not to install VueGen on your system, a pre-configured Docker container is available. It includes all dependencies, ensuring a fully reproducible execution environment. See the [Execution section](#execution) for details on running VueGen with Docker. The official Docker image is available at [quay.io/dtu_biosustain_dsp/vuegen][vuegen-docker-quay].
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### Nextflow and nf-core
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VueGen is also available as a [nf-core][nfcore] module, customised for compatibility with the [Nextflow][nextflow] environment. This module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. The code and documentation for the nf-core module are available in the [nf-VueGen repository][nf-vuegen].
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## Execution
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> [!IMPORTANT]
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> Here we use the `Earth_microbiome_vuegen_demo_notebook` directory and the `Earth_microbiome_vuegen_demo_notebook.yaml` configuration file as examples, which are available in the `docs/example_data` and `docs/example_config_files` folders, respectively. Make sure to clone this reposiotry to access these contents, or use your own directory and configuration file.
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Run VueGen using a directory with the following command:
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These options provide flexibility depending on whether the goal is online accessibility, lightweight execution, or local application distribution.
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## Credits and 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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-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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- VueGen relies on the work of numerous open-source projects like [Streamlit](streamlit), [Quarto][quarto], and others. A big thank you to their authors for making this possible!
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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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## Citation
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If you use VueGen in your research or publications, please cite it as follows:
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**APA:**
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Ayala-Ruano, S., Webel, H., & Santos, A. (2025). *VueGen: Automating the generation of scientific reports*. bioRxiv. https://doi.org/10.1101/2025.03.05.641152
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**BibTeX:**
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```bibtex
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@article{Ayala-Ruano2025VueGen,
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author = {Ayala-Ruano, Sebastian and Webel, Henry and Santos, Alberto},
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title = {VueGen: Automating the generation of scientific reports},
We appreciate your feedback! If you have any comments, suggestions, or run into issues while using VueGen, feel free to [open an issue][new-issue] in this repository. Your input helps us make VueGen better for everyone.
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