What question did this study set out to answer?

The study aims to enhance the process of omics data exploration and minimize errors during analysis.

June 26, 2026Bioinformatics0 citationsOpen Access

Hotgenes: an R package for reducing bottlenecks in bulk omics data exploration and collaboration

Key Points

The study aims to enhance the process of omics data exploration and minimize errors during analysis.
Developed an R package named Hotgenes for modular and flexible utilities.
Implemented a Shiny application for differential expression results sharing among users.
Provided a customizable user interface for advanced users to fit evolving data analysis needs.
Hotgenes enables easy import and sharing of results from bulk omics platforms with minimal coding.
Participants reported a streamlined workflow in data exploration and collaboration.
The application is freely available for users.

Abstract

SUMMARY: A critical part of omics analysis is the transition from early data exploration to final interpretation, often including different analytical platforms and the proliferation of figures, tables, and files. To minimize potential errors and delays that can occur during this process, we have developed an R package called "Hotgenes" that contains a wide range of flexible utilities available in a single modular Shiny application. With Hotgenes, differential expression results generated from bulk omics platforms can be imported and shared among collaborators with minimal coding. Furthermore, the modular Hotgenes user interface can be customized by advanced users to fit the needs of their evolving pipelines. AVAILABILITY AND IMPLEMENTATION: Hotgenes is implemented in R and is freely available at https://github.com/pfizer-opensource/Open-Hotgenes. A permanent archived version is available at https://doi.org/10.5281/zenodo.20129460. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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