aPEAR: an R package for autonomous visualisation of pathway enrichment networks

SummaryThe interpretation of pathway enrichment analysis (PEA) results is frequently complicated by an overwhelming and redundant list of significantly affected pathways. Here, we present an R package aPEAR (Advanced Pathway Enrichment Analysis Representation) which leverages similarities between the pathway gene sets and represents them as a network of interconnected clusters. Each cluster is assigned a meaningful name which highlights the main biological themes in the experiment. Our approach enables automated and objective overview of the data without manual and time-consuming parameter tweaking. Availability and implementationThe package aPEAR is implemented in R, published under the MIT open source licence. The source code, documentation, and usage instructions are available on https://gitlab.com/vugene/aPEAR as well as on CRAN (https://CRAN.R-project.org/package=aPEAR). Contactkerseviciute.ieva@gmail.com or juozas@vugene.com. Supplementary informationThe complete analysis used to evaluate the package can be found at https://github.com/ievaKer/aPEAR-publication.