GSEAplot: A Package for Customizing Gene Set Enrichment Analysis in R
Sarah E. Innis, Kelsie Reinaltt, Mete Civelek, Warren D. Anderson
Abstract
Gene Set Enrichment Analysis (GSEA) is used to identify differentially expressed gene sets that are enriched for annotated biological functions. The existing GSEA R code is not in the form of a flexible package with analysis and plotting customization options, and the results produced are not generated in the form of R objects. In this study, we introduce the GSEAplot R package with novel functionality for saving relevant information from the analysis to the current R workspace, and we introduce the ability to customize plots and databases. The GSEAplot package provides a novel utility that facilitates the implementation of GSEA R-based in genomics analysis pipelines.
Topics & Concepts
R packageComputer sciencePersonalizationSet (abstract data type)WorkspaceComputational biologySource codeBioconductorGenomicsPipeline (software)Programming languageGeneBiologyGenomeWorld Wide WebArtificial intelligenceGeneticsRobotBioinformatics and Genomic NetworksGene expression and cancer classificationGenetic Mapping and Diversity in Plants and Animals