DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

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Exploring Epigenomic Datasets by ChIPseeker (2022, methodology): “Our team has developed several R packages 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…”
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…”
Fast gene set enrichment analysis (2016, background): “That can be done in a straightforward manner by sampling random gene sets as was done in the reference implementation [1] and reimplementations [2, 3].”
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization (2015, methodology): “For functional enrichment analysis, ChIPseeker works fine with in house developed Bioconductor package, clusterProfiler (Yu et al. , 2012), DOSE (Yu et al. , 2015) and ReactomePA.”