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

By Liis Kolberg, Uku Raudvere, I. Kuzmin, Jaak Vilo, Hedi Peterson. F1000Research, 2020

908 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a576e9d0ec218cc3d6742c692acb171aecf432a8

Citations in the corpus

• Using clusterProfiler to characterize multiomics data (2024, critical): “Tools such as GOstats 33 , gprofiler2 34 , DAVID 35 , Enrichr 30 and Metascape 36 only support the ORA algorithm and cannot handle gene ranking lists without specific thresholds.”