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Bio clip seq binding site annotation

Skill FridrichMethod/awesome-skills/skills/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.From its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill bio-clip-seq-binding-site-annotation

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SKILL.md

1.5 KB, 344 tokens by cl100k_base, as published. Nobody here has run it

<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

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-arithmetic - Intersect peaks with genomic features
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it: 2 files

1.4 KB alongside SKILL.md

examples/

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