ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization.

By Guangchuang Yu, Qing‐Yu He. Molecular Biosystems, 2016

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Using clusterProfiler to characterize multiomics data (2024, positive): “By integrating our developed packages such as ReactomePA 17 , meshes 18 , DOSE 19 , GOSemSim 20 and ChIPseeker 21,22 into the framework of clusterProfiler, we have extended the software’s capability to conduct detailed analyses across multiple dimensions, offering insights into biological…”
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data (2021, background): “Besides,there are increasingly morebiologicalknowledgedatabases availablefor exploring functional characteristics from different perspectives, such as Disease Ontology, 24 Reactome Pathway, 25 Medical Subject Headings, 26 , and Wiki-Pathway.”
Exploring Epigenomic Datasets by ChIPseeker (2022, methodology): “…to perform these analyses, including DOSE (Yu, Wang, Yan, & He, 2015) for Disease Ontology analysis (Schriml et al., 2012); ReactomePA (Yu & He, 2016) for the Reactome pathway analysis (Croft et al., 2014); clusterProfiler (Wu, Xu, Guo, & Yu, 2021) for Gene Ontology (GO; Ashburner et al.,…”