Data & ReproStatistics & Data AnalysisFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-chipseq-peak-annotation

Maintainer FreedomIntelligence · Last updated April 1, 2026

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features.

OpenClawNanoClawAnalysisReproductionbio-chipseq-peak-annotation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinannotate

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-peak-annotation

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

R: ChIPseeker::annotatePeak(peaks, TxDb=txdb).
Annotate my ChIP-seq peaks to genes" → Assign peaks to genomic features (promoter, exon, intron, intergenic), find nearest genes, and calculate TSS distances. R: ChIPseeker::annotatePeak(peaks, TxDb=txdb).
peaks <- readPeakFile('sample_peaks.narrowPeak').

Source Doc

Excerpt From SKILL.md

Load Peaks and Annotations

library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

## Annotate Peaks

**Goal:** Assign each ChIP-seq peak to its nearest gene and genomic feature category.

**Approach:** Use annotatePeak with a TxDb annotation database to classify peaks as promoter, exon, intron, or intergenic and retrieve the nearest gene symbol.

```r

## Annotate with default settings

peak_anno <- annotatePeak(
    peaks,
    TxDb = txdb,
    annoDb = 'org.Hs.eg.db'
)