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Related Experiment Video

Updated: Jun 13, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Lihua J Zhu¹, Claude Gazin, Nathan D Lawson

¹Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. julie.zhu@umassmed.edu

BMC Bioinformatics

|May 13, 2010

Summary

This summary is machine-generated.

ChIPpeakAnno is an R package for easy batch annotation of DNA-binding sites from ChIP-seq and ChIP-chip experiments. It simplifies summarizing large datasets and visualizing genomic regions for further analysis.

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Last Updated: Jun 13, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data

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Published on: December 13, 2024

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Chromatin immunoprecipitation sequencing (ChIP-seq) and ChIP-chip are standard for identifying DNA-binding protein targets genome-wide.
Existing algorithms identify binding sites but summarizing large datasets is challenging.

Purpose of the Study:

To develop an R package, ChIPpeakAnno, for efficient batch annotation of enriched genomic regions.
To facilitate the analysis and visualization of large-scale ChIP-seq and ChIP-chip data.

Main Methods:

Developed ChIPpeakAnno as a Bioconductor package in R.
Implemented functionalities for batch annotation, visualization (tables, charts, histograms), overlap analysis, sequence retrieval, and Gene Ontology term association.

Main Results:

ChIPpeakAnno facilitates batch annotation of enriched peaks from ChIP-seq, ChIP-chip, and CAGE.
Provides versatile visualization options and enables overlap analysis between replicates or transcription factors.
Includes tools for retrieving flanking sequences and identifying associated Gene Ontology terms.

Conclusions:

ChIPpeakAnno streamlines the annotation of large genomic datasets from various high-throughput experiments.
Offers flexibility through user-provided annotation data and integration with biomaRt for up-to-date annotations.