bio-chipseq-peak-annotation
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-peak-annotation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: MACS3 3.0+, clusterProfiler 4.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Peak Annotation with ChIPseeker **"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)` ## Load Peaks and Annotations ```r library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(org.Hs.eg.db) txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene # Read peaks from MACS3 peaks <- readPeakFile('sample_peaks.narrowPeak') ``` ## 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_a
- Version Compatibility
- Load Peaks and Annotations
- Annotate Peaks
- Custom Promoter Definition
- Extract Annotated Data Frame
- Get Genes with Peaks in Promoter
- Annotation Pie Chart
- Distance to TSS Plot
- Compare Multiple Peak Sets
- Venn Diagram of Peak Overlap
- Coverage Plot
- Profile Heatmap Around TSS
- Functional Enrichment of Peak Genes
- Seq2Gene - All Genes in Peak Regions
What does the bio-chipseq-peak-annotation skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-peak-annotation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.