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gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler

2020; Faculty of 1000; Volume: 9; Linguagem: Inglês

10.12688/f1000research.24956.2

2046-1402

Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson,

RNA modifications and cancer

g:Profiler ( https://biit.cs.ut.ee/gprofiler ) 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, gprofiler2 , developed to facilitate programmatic access to g:Profiler computations and databases via REST API. The gprofiler2 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, gprofiler2 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 gprofiler2 package is freely available at the CRAN repository .