gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Abstract
<ns3:p> g:Profiler ( <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="http://biit.cs.ut.ee/gprofiler">https://biit.cs.ut.ee/gprofiler</ns3:ext-link> ) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, <ns3:bold>gprofiler2</ns3:bold> , developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The <ns3:bold>gprofiler2</ns3:bold> package provides an easy-to-use functionality that enables researchers to incorporate functional enrichment analysis into automated analysis pipelines written in R. The package also implements interactive visualisation methods to help to interpret the enrichment results and to illustrate them for publications. In addition, <ns3:bold>gprofiler2</ns3:bold> gives access to the versatile gene/protein identifier conversion functionality in g:Profiler enabling to map between hundreds of different identifier types or orthologous species. The <ns3:bold>gprofiler2</ns3:bold> package is freely available at the <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri" ns4:href="https://cran.r-project.org/package=gprofiler2">CRAN repository</ns3:ext-link> . </ns3:p>