# Bioconductor Chipseeker

ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Data and ML
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-chipseeker -g -a gemini-cli -y`

## Description

ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# ChIPseeker, Comprehensive Skill Guide

> **Domain:** ChIP-seq / ATAC-seq
> **Bioconductor:** [ChIPseeker](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html)
> **Paper:** Yu G, Wang LG, He QY (2015). Bioinformatics, 31(14):2382-2383.

ChIP-seq peak annotation, comparison, and visualization. Annotates peaks to nearest genomic features, generates coverage and TSS profile plots.

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

- **Version:** 1.48.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Imports:** AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, gtools, magrittr, plotrix, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, yulab.utils
- **Install:** `BiocManager::install("ChIPseeker")`

## When to Use

- Annotate ChIP-seq/ATAC-seq peaks to promoters, exons, introns, intergenic regions
- Profile read coverage around TSS (transcription start sites)
- Compare peak sets across experiments
- Functional enrichment of annotated peaks

**Alternatives:** `HOMER annotatePeaks.pl`, `GREAT (web tool)`, `GenomicFeatures`

## Do NOT Use When

- Differential binding analysis (use DiffBind or csaw).
- Motif analysis (use MEME-ChIP, HOMER, or universalmotif).
- De novo peak calling, peaks must already be called (MACS2, HOMER, etc.).

## Data Requirements

| Requirement | Details |
|-------------|----------|
| **Input Format** | BED/narrowPeak files, or GRanges objects of called peaks |
| **Annotation Db** | TxDb (e.g. TxDb.Hsapiens.UCSC.hg38.knownGene) + OrgDb (org.Hs.eg.db) |
| **Genome Match** | Peak genome assembly must match TxDb genome assembly exactly |

## Installation

```r
if (!require("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ChIPseeker")
library(ChIPseeker)
```

## Workflows

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/epigenomics/chipseeker/SKILL.md