Abstract
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.
Highlights
Interpretation of gene lists is a key step in numerous biological data analysis workflows, such as differential gene expression analysis and co-expression clustering of RNA-seq or microarray data
G:Profiler is a popular web toolset that helps to handle gene lists from various biological and biomedical studies of more than 600 species and strains, including vertebrates, plants, fungi, insects and parasites1,2. g:Profiler’s best known functionality is the over-representation analysis to identify significantly enriched biological functions and pathways obtained from well established data sources which include, among others, Gene Ontology (GO)[3], KEGG4 and Reactome[5]
After creating an instance of the enrichResult or compareClusterResult class from the gost result, this object can be used as an input for the visualisation functions from enrichplot and clusterProfiler that are suitable for over-representation analysis such as dotplot, barplot, cnetplot, upsetplot, emapplot, etc
Summary
2. Ewy Mathe , National Center for Advancing Translational Sciences/National Institutes of Health, Bethesda, USA. Any reports and responses or comments on the article can be found at the end of the article. This article is included in the ELIXIR gateway. This article is included in the RPackage gateway
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