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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.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
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正在显示 SKILL.md
| name | bio-clip-seq-binding-site-annotation |
| description | 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. |
| tool_type | mixed |
| primary_tool | ChIPseeker |
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)
# Annotate to UTRs
bedtools intersect -a peaks.bed -b 3utr.bed -wa -wb > peaks_3utr.bed
import pandas as pd
def annotate_peaks(peaks_bed, annotation_gtf):
'''Annotate peaks to genomic features'''
# Load peaks and annotations
# Intersect and categorize
pass