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bioRxiv · 10.1101/2023.03.28.534514

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

Kerseviciute, I.·Gordevicius, J.
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Abstract

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.

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Kerseviciute, I., Gordevicius, J.. 2023-03-29. aPEAR: an R package for autonomous visualisation of pathway enrichment networks. https://doi.org/10.1101/2023.03.28.534514

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