ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

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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, methodology): “Our in-house developed package, ChIPseeker, 10 is originally designed for chromatin immunoprecipitation (ChIP) peak annotation, comparison, and visualization and has been employed to analyze genome-wide ROIs, such as open chromatin regions obtained by DNase-seq 32 and ATAC-seq.”
MIR sequences recruit zinc finger protein ZNF768 to expressed genes (2018, methodology): “Annotation of peaks relative to gene features was performed using the ChipSeeker package in R (40).”
Missense variants causing Wiedemann-Steiner syndrome preferentially occur in the KMT2A-CXXC domain and are accurately classified using AlphaFold2 (2022, neutral): “251 Differential peaks obtained in DiffBind were given genomic annotations and converted to 252 GRanges objects using the ChIPseeker package in R [25].”