README.Rmd

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# multienrichjam

The goal of multienrichjam is to implement MultiEnrichMap,
an extension to EnrichMap and Enrichment Map, originally
envisioned and implemented as a Cytoscape plugin by the
lab of Dr. Gary Bader

* Bader lab [EnrichmentMap](https://www.baderlab.org/Software/EnrichmentMap), and
* reference: [Merico,et al, PLoS One, 2010](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013984)),

and re-implemented into a larger analysis workflow in R
by Dr. Guangchuang Yu in the R packages:

* [clusterProfiler](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html), and
* [enrichplot](https://bioconductor.org/packages/release/bioc/html/enrichplot.html).

The MultiEnrichMap extension is a relatively straightforward set
of functions to help enable comparison of enrichment results from multiple
gene set enrichment tests.


## Package Reference

A full online function reference is available via the pkgdown
documentation:

[Full multienrichjam command reference](https://jmw86069.github.io/multienrichjam)


## How to install

Install using the R package `remotes` and this command:

```
remotes::install_github("jmw86069/multienrichjam",
   dependencies=TRUE);
```



If you do not have the `remotes` package, you can install it from CRAN:

```
install.packages("remotes");
```

Note that we changed the recommended installation from using `devtools`
to using `remotes` because the `remotes` package is much smaller
with fewer dependencies.