PathwayVolcano tool

[thoconne]

[Submission] PathwayVolcano

Package Information

• Package Name: PathwayVolcano
• Short Description: An R package for visualizing pathway enrichment results using volcano plots.
• GitHub Repository: https://github.com/thoconne/PathwayVolcano
• Bioconductor Maintainer: Thomas O'Connell <[email protected]>

Summary of the Package

PathwayVolcano is an R package that provides interactive volcano plots for pathway enrichment analysis. It allows researchers to:

• Visualize pathway significance vs. fold-change data.
• Highlight significant pathways dynamically.
• Customize plots for publication-ready figures.

The package is designed to work with Bioconductor enrichment analysis tools, such as clusterProfiler and ReactomePA.

R CMD Build and Check

Results from R CMD Check (on R-devel):

• ✅ No ERRORS
• ✅ No WARNINGS
• ✅ No NOTES

* checking package dependencies ... OK
* checking installed package size ... NOTE
  installed size is 5.1Mb
* checking R code for possible problems ... OK

Bioconductor Compliance

• ✅ BiocCheck::BiocCheckGitClone("PathwayVolcano") passes without errors.
• ✅ Package follows Bioconductor coding standards.
• ✅ Includes a vignette and unit tests.

Additional Comments

• This package was inspired by pathway visualization limitations in existing Bioconductor tools.
• The package provides high-resolution plots with ggplot2 and plotly interactivity.
• I am open to feedback and improvements based on the Bioconductor review.

Maintainer Confirmation

I confirm that:

• I have read the Bioconductor Package Submission Guidelines.
• My package follows Bioconductor best practices.
• I am prepared to actively maintain this package.

Next Steps

Once submitted, a Bioconductor reviewer will:

1. Verify package structure & dependencies.
2. Run additional compliance checks.
3. Provide review comments (typically within 2-6 weeks).
4. Approve package after revisions.