Agent skill
bio-clip-seq-binding-site-annotation
Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
Install this agent skill to your Project
npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/data/binding-site-annotation
SKILL.md
Binding Site Annotation
Using ChIPseeker (R)
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
peaks <- readPeakFile('peaks.bed')
anno <- annotatePeak(peaks, TxDb = txdb)
plotAnnoPie(anno)
Using BEDTools
# Annotate to UTRs
bedtools intersect -a peaks.bed -b 3utr.bed -wa -wb > peaks_3utr.bed
Python Annotation
import pandas as pd
def annotate_peaks(peaks_bed, annotation_gtf):
'''Annotate peaks to genomic features'''
# Load peaks and annotations
# Intersect and categorize
pass
Related Skills
- clip-peak-calling - Get peaks
- genome-intervals - Interval operations
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