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SummArIzeR

SummArIzeR is an R package, that allows an easy use of EnrichR to compare enrichment results from multiple databases of multiple conditons. It results in a clustering of enriched terms and enables the annotation of these terms by creating a promt for large language models such as gpt4. Results can be vizualised in a Heatmap.

Features

  • Perform enrichment analysis using enrichR.
  • Allows analysis of multiple conditions
  • Analyze up- and down-regulated genes separately.
  • Filter terms by p-value and gene thresholds.
  • Calculates similarities of results terms based on included genes
  • Clusters terms using random walk algorithm
  • Generates a prompt for a LLM to summarized cluster annotations
  • Allows easy visualization

Workflow

Steps to perform an enrichment analysis with SummArIzeR:

  • Enrichment analysis
  • Treshold selection for Term clustering
  • Term annotation using LLMs
  • Vizualisation

Citation

If you are using SummArIzeR for your publication, please cite us:

SummArIzeR: Simplifying cross-database enrichment result clustering and annotation via large language models Marie Brinkmann, Michael Bonelli, Anela Tosevska bioRxiv 2025.05.28.656331; doi: https://doi.org/10.1101/2025.05.28.656331

Bug Reports

If you encounter any errors or issues, or if you have a suggestion please file an issue here.