gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• g:Profiler has been a key tool for gene list functional profiling and identifier conversion since 2007.
• Reproducible biological data analysis relies on accessible and integrated computational tools.

Purpose of the Study:

• Introduce the gprofiler2 R package for programmatic access to g:Profiler.
• Facilitate the integration of functional enrichment analysis into automated R-based pipelines.
• Provide enhanced visualization tools for enrichment results.

Main Methods:

• Development of an R package (gprofiler2) interfacing with the g:Profiler REST API.
• Implementation of functions for gene list enrichment analysis.
• Inclusion of interactive visualization methods for results interpretation.
• Integration of gene/protein identifier mapping capabilities.

Main Results:

• gprofiler2 enables seamless programmatic access to g:Profiler's extensive databases and functionalities.
• The package simplifies the incorporation of functional enrichment analysis into automated R workflows.
• Interactive visualizations aid in the interpretation and presentation of enrichment findings.
• Access to versatile gene and protein identifier conversion across multiple species and ID types is provided.

Conclusions:

• The gprofiler2 R package significantly enhances the utility of g:Profiler for researchers.
• It promotes reproducible and automated biological data analysis.
• Freely available on CRAN, gprofiler2 supports the broader scientific community.