Visualization and interpretation of functional and literature enrichment analysis results from multiple sets.
Flame is a web application (R/Shiny + JavaScript) for comprehensive enrichment analysis. It allows you to upload various input types, combine and compare sets, run functional and literature enrichments through multiple tools, and visualize results interactively.
- Multiple Input Types: Gene/protein lists, SNPs, free text, or expression results (volcano plots).
- Set Operations: Union and intersection of lists with UpSet plots.
- Functional Enrichment: Supports aGOtool, gProfiler, WebGestalt, and enrichR across 14,000+ organisms.
- Literature Enrichment: Powered by aGOtool.
- Network Integration: Generate STRING protein–protein interaction networks.
- Visualization Options: Networks, heatmaps, bar charts, scatter plots, and searchable tables.
- Network Analysis: Gene–function, function–function, and gene–gene association levels.
- Interactive 3D Views: Multi-layered network visualization via Arena3Dweb.
- Filtering & Integration: Combine sources and apply interactive filters.
- ID Conversions: Cross-database and cross-species.
- API Access: Integrate Flame with external applications.
# Pull the Flame image
docker pull pavlopouloslab/flame
# Run the container
docker run -p 3838:3838 pavlopouloslab/flame-
Clone the repository:
git clone https://github.com/PavlopoulosLab/Flame.git cd Flame
2. Ensure R (>=4.0) and RStudio are installed.
3. Install required R packages:
```r
install.packages(c(
"shinyjs", "shinyalert", "bsplus", "upsetjs", "stringr",
"httr", "httpuv", "curl", "jsonlite", "gprofiler2",
"WebGestaltR", "shinydashboard", "shinyWidgets", "DT",
"tidyr", "enrichR", "plotly", "igraph", "visNetwork"
))
- Open Flame.Rproj in RStudio.
- Open server.R, select Run External, then click Run App.
Access the web interface at http://flame-enrich.org or run locally as above. Upload your data, explore enrichment analyses, and customize visualizations using the intuitive UI.
-
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources Karatzas E., Baltoumas F.A., Aplakidou E., Kontou P.I., Stathopoulos P., Stefanis L., Bagos P.G., Pavlopoulos G.A. Bioinformatics. 2023 Aug;39(8):btad490. doi: 10.1093/bioinformatics/btad490
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FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists Thanati F., Karatzas E., Baltoumas F.A., Stravopodis D.J., Eliopoulos A.G., Pavlopoulos G.A. Biology. 2021 Jul;10(7):665. doi: 10.3390/biology10070665
This project is licensed under the MIT License – see the LICENSE file for details.