Reporting with VueGen

VueGen is a tool that automates the creation of reports from bioinformatics outputs, allowing researchers with minimal coding experience to communicate their results effectively.

With VueGen, users can produce reports by simply specifying a directory containing output files, such as plots, tables, networks, Markdown text, HTML components, and API calls, along with the report format. Supported formats include documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), Jupyter notebooks, and Streamlit web applications.

In the GitHub workspace, we will use the base conda environment, which you can activate with the following command:

python -m venv vuegen
source vuegen/bin/activate

Install the required packages

• VueGen for the report generation (developed by Henry Webel from DSP and Sebastian Ayala and Alberto Santos from MoNA at DTU Biosustain)

pip install vuegen

VueGen Report

We saved some of the analyses (plots and tables) from the R markdown files in the results/report folder.

You can use the following command to generate a VueGen report (Streamlit web application in this case) from them:

vuegen --directory results/report --report_type streamlit 

This will create the scripts to build a Streamlit web application in the streamlit_report folder. Now, you can run the app with the following command:

streamlit run streamlit_report/sections/report_manager.py

You can check additional report types supported by VueGen, and other options with the following command:

vuegen -h

Further information about VueGen

If you are interested to know more about VueGen and use it for your own research projects, check out its GitHub repository, some tutorials in YouTube tutorials on youtube, and also our biorxiv paper.