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

TLDR

ChIPseeker is an R package designed for annotating ChIP‑seq data analysis. It annotates ChIP peaks, visualizes peak coverage and TSS binding profiles, compares peak profiles and annotations, and evaluates significant overlap among ChIP‑seq datasets. The package contains 15,000 BED files from the GEO database, enabling users to download and compare them with their own data to identify significant overlaps that suggest co‑regulation or transcription factor complexes. ChIPseeker is released under the Artistic‑2.0 License, with source code and documentation available on Bioconductor, and contact emails [e-mail] and [e-mail] for support.

Abstract

Abstract Summary: ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with user’s own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation. Availability and implementation: ChIPseeker is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html). Contact: [e-mail] or [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.