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bio-clip-seq-clip-peak-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

Call RBP binding peaks from CLIP-seq with PureCLIP or MACS2.

OpenClawNanoClawAnalysisReproductionbio-clip-seq-clip-peak-calling🧠 bioos extended suitebioos extended bioinformatics suitecall

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-clip-seq-clip-peak-calling

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

clipper \ -b deduped.bam \ -s hg38 \ -o peaks.bed \ --save-pickle.
clipper \ -b deduped.bam \ -s hg38 \ -o peaks.bed \ --FDR 0.05 \ --superlocal.

Source Doc

Excerpt From SKILL.md

Specify gene annotations

clipper
-b deduped.bam
-s hg38
--gene genes.bed
-o peaks.bed


## CLIPper Options

| Option | Description |
|--------|-------------|
| -b | Input BAM file |
| -s | Species (hg38, mm10) |
| -o | Output BED file |
| --FDR | FDR threshold (default 0.05) |
| --superlocal | Use superlocal background |
| --gene | Custom gene annotation BED |
| --save-pickle | Save intermediate data |

## PureCLIP (HMM-Based)

PureCLIP uses an HMM to model crosslink sites, incorporating enrichment and truncation signals.

```bash

Use cases

Use bio-clip-seq-clip-peak-calling for genomics and bioinformatics workflows.
Apply bio-clip-seq-clip-peak-calling to sequencing, variant, or omics analysis tasks.