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bio-chipseq-peak-annotation
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-chipseq-peak-annotation：Annotate ChIP-seq peaks to genomic features 、 genes ，使用 ChIPseeker。 Assign peaks to promoters，exons，introns，、 intergenic regions。 适合在annotating ChIP-seq peaks to genomic features时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-peak-annotation
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 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，、 calculate TSS distances. R：ChIPseeker：：annotatePeak(peaks，TxDb=txdb)。
- peaks <- readPeakFile('sample_peaks.narrowPeak')。
原始文档
SKILL.md 摘录
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'
)
适用场景
- 适合在annotating ChIP-seq peaks to genomic features时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- peak-calling - Generate peak files with MACS3
- differential-binding - Find differential peaks
- pathway-analysis - Functional enrichment
- chipseq-visualization - Additional visualizations
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