chip-seq
ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.
npx skills add BioTender-max/awesome-bio-agent-skills --skill chip-seq --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.
# ChIP Seq ## Version Compatibility Reference examples assume: - `macs3` 3.0+ - `samtools` 1.18+ - `deepTools` 3.5+ Before using commands, verify the installed environment: - CLI: `macs3 --version`, `samtools --version`, `bamCoverage --version` - If flags differ, inspect `--help` and adapt rather than forcing the example unchanged. ## Overview Use this skill for: - narrow or broad peak calling - input-normalized signal tracks - peak annotation - motif follow-up - differential binding review when replicates exist ## When To Use This Skill - the user has aligned ChIP and optional input BAM files - the deliverable includes peaks, browser tracks, or motif results - the assay is TF ChIP or histone-mark ChIP and needs standard peak-centric processing ## Quick Route - TF or narrow marks: use narrow peak mode first. - H3K27me3, H3K36me3, or other broad marks: use `--broad`. - Paired-end BAM: prefer `-f BAMPE`. - No input control: still possible, but report the limitation explicitly. ## Progressive Disclosure - Read [technical_reference.md](technical_reference.md) for QC gates, narrow-versus-broad logic, and replicate handling. - Read [commands_and_thresholds.md](commands_and_thresholds.md)
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Prerequisites
- Expected Inputs
- Expected Outputs
- Starter Pattern
- Key Parameters
- Workflow
- 1. Validate BAMs and replicate structure
- 2. Call peaks with MACS3
- 3. Export signal tracks
macs3 callpeak \
What does the chip-seq skill do?
ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill chip-seq --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.