vivid-volcano - Vivid Volcano: Empowering Non-Bioinformaticians to1 Analyze Pre-Processed Omics Data

Full Changelog: https://github.com/DatViseR/Vivid-Volcano/compare/v1.0.0...v1.0.1 Paper figures where updated to high resolution panel figures. Zenodo source code repository title was changed in the readme.

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Published by DatViseR 6 months ago

vivid-volcano - Vivid Volcano v1.0 - an intuitive tool that helps experimental scientists with no bioinformatics background explore and analyze pre-processed omics data.

This is the version of Vivid Volcano after completion of the review process in the Journal of Open Source Software

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Published by DatViseR 7 months ago

vivid-volcano - v0.1.4

I have greatly improved the automatic universal installation script as well as the main README.md documentation. The new installer and documentation are designed to make both standard and advanced deployments as smooth as possible for all users, whether on Linux, macOS, or in cloud/container environments (e.g., GitHub Codespaces).

Key improvements:

Truly universal installer: The new script automatically detects your environment (Linux, macOS, or container) and guides you through the installation process with clear steps and progress indicators.

Optional system dependencies: The script now offers the option to install system libraries (such as Cairo) that are not required for basic app functionality but can enhance features (like high-quality PDF outputs or advanced table formatting). This means you can perform a minimal install or opt-in to advanced features as needed.

Full local reproducibility: I have tested the automatic installation in clean local environments (Linux and macOS) as well as in GitHub Codespaces (Ubuntu container). The script ensures Vivid Volcano can be installed and run in a completely fresh system without manual intervention.

Improved R package handling: The script automatically detects if system-level libraries (like Cairo) are available and only installs R packages that will work in your environment. If Cairo is not available, the app still installs and runs with all its core features.

macOS-specific issues resolved:

1. Browser not opening when using R -e "shiny::runApp()"

The README now documents this common macOS issue and provides several easy solutions, including using the new ./launchapp.sh or R -f launchapp.R launchers, which have enhanced browser opening support and multiple fallbacks for different macOS setups. Manual browser launch instructions are also included as a last resort.

1. Cairo installation on macOS (and Linux):

The installer now clearly explains that Cairo is optional, and offers to install it via Homebrew (macOS) or apt/dnf (Linux). If it is not installed or fails to build, the script will still complete and the app will run, but with a notification that some enhanced graphics features may not be available. The script also auto-detects the presence of Cairo and only attempts to install the R Cairo package if the underlying system library is found.

Documentation updates:

The [README.md](https://github.com/DatViseR/Vivid-Volcano/blob/master/README.md) now includes detailed, step-by-step installation instructions for UNIX (Linux/macOS/container/cloud environments) and Windows.

Troubleshooting tips for browser launching, Cairo/graphics support, and other common issues are now covered with practical solutions.

Clear distinction between core (essential for running the app) and enhanced (optional, for advanced output or developer use) dependencies.

Manual installation instructions are also provided for users who prefer or require more control.

Summary: The new installer and documentation make it much easier to deploy Vivid Volcano everywhere, minimize setup problems, and offer a much better installation experience. If you previously encountered issues with browser launching or Cairo installation, these should now be resolved or clearly documented with actionable solutions.

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Published by DatViseR 8 months ago

vivid-volcano - Vivid Volcano v0.1.3 - an intuitive tool that helps experimental scientists with no bioinformatics background explore and analyze pre-processed omics data.

• Detailed local installation guidelines were introduced to documentation
• Automatic installation script for UNIX systems was developed
• Detailed instructions and community guidelines for contributions were created

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Published by DatViseR 9 months ago

vivid-volcano - DatViseR/Vivid-Volcano - an intuitive tool that helps experimental scientists with no bioinformatics background explore and analyze pre-processed omics data. Pre-release. (v0.1.2)

• This patch includes corrected references to the publication file about Vivid Volcano

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Published by DatViseR 10 months ago

vivid-volcano - Vivid Volcano v0.1.1 - an intuitive tool that helps experimental scientists with no bioinformatics background explore and analyze pre-processed omics data.

This pre-release patch improves the speed of file uploads and increased their size to 40MB.

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Published by DatViseR 10 months ago

vivid-volcano - Vivid Volcano v0.1.0 - an intuitive tool that helps experimental scientists with no bioinformatics background explore and analyze pre-processed omics data.

This is the first release linked with Zenodo DOI and a DOI for a preprint of a journal publication about Vivid Volcano. The app is after a long round of closed beta testing.

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Published by DatViseR 11 months ago