EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Enrichment analysis identifies biological pathways or gene sets associated with phenotypes.
• Current tools are limited to predefined gene sets from public databases.
• Flexible analysis of custom gene sets and complex data is needed.

Purpose of the Study:

• Introduce EnrichIntersect, an R package for flexible enrichment analysis.
• Enable enrichment analysis using user-defined custom sets.
• Provide interactive visualization for multiple covariates and phenotypes.

Main Methods:

• Developed an R package named EnrichIntersect.
• Implemented functionality for enrichment analysis with custom sets.
• Integrated interactive visualization for multiple features and sample groups.

Main Results:

• EnrichIntersect supports enrichment analysis with any ranked features and user-defined custom sets.
• The package offers interactive visualization of associations between multiple covariates and phenotypes.
• It clearly indicates intersecting covariates across multiple phenotypic variables and sample groups.

Conclusions:

• EnrichIntersect enhances the flexibility of enrichment analysis.
• The package facilitates the exploration of complex biological associations.
• It aids in identifying intersecting biological features across diverse phenotypes and sample groups.