README.md
<!-- badges: start -->[](https://github.com/adeschen/enrichViewNet/actions/workflows/check-bioc.yml)[](https://codecov.io/gh/adeschen/enrichViewNet)[](https://opensource.org/licenses/Artistic-2.0)<!-- badges: end -->The **enrichViewNet** package enables the transformation of functional enrichment results, formatted as the results obtained by [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html), into networks. First, the **enrichViewNet** package enables the visualization of enrichment results a [Cytoscape](https://cytoscape.org/) network where significant terms (Gene Ontology/Reactome/Transcription Factor/etc..) and genes are nodes. In this network, edges connect genes that are part of theenrichment request to their terms. In addition, the **enrichViewNet** package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps, as introduced in the Bioconductor [enrichplot](https://bioconductor.org/packages/release/bioc/html/enrichplot.html) package, enable the visualization of enriched terms into a network with edges connecting overlapping genes. Thus, enriched terms with overlapping genes cluster together.## Bioconductor Package ##[](https://bioconductor.org/packages/enrichViewNet)The **enrichViewNet** package is now an official package of [Bioconductor](http://bioconductor.org/). The current Bioconductor release can be directly downloaded from their website:[Current release](https://bioconductor.org/packages/enrichViewNet/)## Authors ##[Astrid Deschênes](http://ca.linkedin.com/in/astriddeschenes "Astrid Deschênes"), [Pascal Belleau](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau"), [Robert L Faure](https://www.crchudequebec.ulaval.ca/en/research/researchers/robert-l-faure/), [Maria J Fernandes](https://www.crchudequebec.ulaval.ca/en/research/researchers/maria-fernandes/),[Alexander Krasnitz](https://www.cshl.edu/research/faculty-staff/alexander-krasnitz/) and [David A Tuveson](https://tuvesonlab.labsites.cshl.edu/)## License ##This package and the underlying **enrichViewNet** code are distributed under the Artistic license 2.0. You are free to use and redistribute this software. For more information on Artistic 2.0 License see[http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)## Documentation ##[enrichViewNet Website](https://adeschen.github.io/enrichViewNet/)[enrichViewNet Get Started](https://adeschen.github.io/enrichViewNet/articles/enrichViewNet.html)## Installation ##To install the latest version accessible, the [devtools](https://cran.r-project.org/web/packages/devtools/index.html) package is required. ## Load required package library(devtools) ## Install the latest version of enrichViewNet devtools::install_github('adeschen/enrichViewNet')To install this package from [Bioconductor](https://bioconductor.org), start R (version 4.3 or later) and enter: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("enrichViewNet")## Bugs/Feature requests ##If you have any bugs or feature requests, [let us know](https://github.com/adeschen/enrichViewNet/issues). Thanks!
