VueGen: automating the generation of scientific reports

TL;DR

VueGen is a tool that automates the creation of scientific reports from bioinformatics data, making it easier for researchers to communicate their findings without needing advanced technical skills.

Contribution

VueGen introduces an automated reporting system that supports multiple output formats and requires minimal user input.

Findings

VueGen can generate reports in various formats including PDF, HTML, and presentations.

The tool is accessible as a Python package, Docker image, and desktop application.

Case studies demonstrate its effectiveness in streamlining scientific reporting workflows.

Abstract

The analysis of omics data typically involves multiple bioinformatics tools and methods, each producing distinct output files. However, compiling these results into comprehensive reports often requires additional effort and technical skills. This creates a barrier for non-bioinformaticians, limiting their ability to produce reports from their findings. Moreover, the lack of streamlined reporting workflows impacts reproducibility and transparency, making it difficult to communicate results and track analytical processes.

We present VueGen, 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, and HTML components, along with the report format. Supported formats include documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), Jupyter notebooks, and Streamlit web applications. To showcase VueGen’s functionality, we present two case studies and provide detailed documentation to help users generate customized reports.

VueGen is distributed as a Python package, Docker image, nf-core module, and desktop application. The source code is freely available on https://github.com/Multiomics-Analytics-Group/vuegen under the MIT license. Documentation is provided at https://vuegen.readthedocs.io/.

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