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.
Profile →npx skills add majiayu000/claude-skill-registry --skill 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.
# Peak Annotation with ChIPseeker ## 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 MACS2 peaks <- readPeakFile('sample_peaks.narrowPeak') ``` ## Annotate Peaks ```r # Annotate with default settings peak_anno <- annotatePeak( peaks, TxDb = txdb, annoDb = 'org.Hs.eg.db' ) # View annotation summary peak_anno ``` ## Custom Promoter Definition ```r # Define promoter region (-3kb to +3kb from TSS) peak_anno <- annotatePeak( peaks, TxDb = txdb, tssRegion = c(-3000, 3000), # Promoter definition annoDb = 'org.Hs.eg.db' ) ``` ## Extract Annotated Data Frame ```r # Convert to data frame anno_df <- as.data.frame(peak_anno) # Key columns: seqnames, start, end, annotation, distanceToTSS, SYMBOL, GENENAME head(anno_df) # Export to CSV write.csv(anno_df, 'annotated_peaks.csv', row.names = FALSE) ``` ## Get Genes with Peaks in Promoter ```r # Filter for promoter peaks promoter_peaks <- anno_df[grep('Promoter', anno_df$annotation), ] # Get unique genes promoter_genes <- unique(promoter_peaks$SYMBOL) ``` ## Annotation Pie Chart ```r # Pie chart of genomic feature distribu
- 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
- Different Organisms
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 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 majiayu000/claude-skill-registry, a repository with 534 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.