Individual skill
chip-seq-analysis
ChIP-seq analysis — peak calling, differential binding, motif discovery, and QC with phantom-peak metrics.
skills/chip-seq-analysis/SKILL.md
Source commit faf37c0859ebf627bfcb5225e8057d088691e0ae
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Instructions only
- Last checked
- Nov 8, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 53
- Repository last updated
- Oct 10, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- agent-skills Repository topic
- ai-agents Repository topic
- ai-agents-automation Repository topic
- ai-skills Repository topic
- awesome Repository topic
- awesome-list Repository topic
- chatgpt Repository topic
- claude-skills Repository topic
- meta-ai Repository topic
- muse-ai Repository topic
- engineering Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Read excerpt
## Overview
chip-seq-analysis covers chromatin immunoprecipitation sequencing from raw reads to biological
interpretation: QC specific to ChIP (fragment size, enrichment metrics), peak calling (MACS2),
differential binding (DiffBind/DESeq2), motif discovery, and annotation of peaks to regulatory
function. ChIP-seq quality is dominated by the antibody — the analysis can only work with what
the IP enriched.
## When to use
- Experimental design: antibody validation, controls (input/IgG), replicate numbers, depth.
- QC: cross-correlation, FRiP, library complexity, strand cross-correlation.
- Peak calling: MACS2 parameters for narrow (TFs) vs broad (histone marks) peaks.
- Differential binding: DiffBind, proper count-based statistics.