> For the complete documentation index, see [llms.txt](https://gseacompass.gitbook.io/user-manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://gseacompass.gitbook.io/user-manual/gseacompass.md).

# GSEACompass

## What it is and what it's not

GSEACompass is a software intended to

* Provide a quick and straight-forward way of running [GSEA, GSEA preranked](https://pmc.ncbi.nlm.nih.gov/articles/PMC1239896/), [ssGSEA](https://gsea-msigdb.github.io/ssGSEA-gpmodule/v10/index.html) and [GSVA](https://www.bioconductor.org/packages/release/bioc/html/GSVA.html);
* Generate, resize and save many publication-ready graphical representations of obtained data, such as:
  * **Enrichment plot** on single or multiple gene sets;
  * **Dotplot** on any numerical field, on multiple gene sets;
  * **Heatmap** on a single gene set, or on the entire output of ssGSEA and GSVA;
  * **Intersection over union** of gene sets with respect to the leading genes;
  * **Wordcloud** on any textual field (gene set name or leading genes), on multiple gene sets;
  * **Similarity graph**, in the embedding space of a BERT-like model, of multiple gene set names;
  * **Similarity heatmap**, in the embedding space of BERT-like model, of multiple geneset names;
* Streamline the activity of searching meaningful data amongst the plentiful output of GSEA;
* Avoid the, sometimes tedious and error-prone, task of doing post-analyses by writing code, providing a clean GUI that does it for you.

On the other hand, GSEACompass doesn't want to replace the [official MSigDB GSEA software](https://www.gsea-msigdb.org/gsea/downloads.jsp), but rather be a worthy addition, mostly aimed at speeding up the process of extracting meaningful information and visualizations from GSEA output.

Watch this [video](https://www.youtube.com/watch?v=H2Jo8MZXmUI), if you want to see a practical use-case of GSEACompass. 

If you'd like to build a GSEACompass executable on your own, read the [README](https://github.com/DEIB-GECO/GSEACompass/blob/main/README.md) of the official Github repository.

## Stability

In case it doesn't behave has supposed, feel free to open a pull-request on the [Github repository](https://github.com/DEIB-GECO/GSEAWrap/pulls).