macs3-peak-calling SKILL.md skillA
macs3-peak-calling from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/macs3-peak-calling@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/macs3-peak-calling/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- Feb 18, 2026
- Size
- 13,892 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; broad for H3K27me3, H3K9me3, and other broad marks.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# MACS3 — ChIP-seq and ATAC-seq Peak Caller ## Overview MACS3 (Model-based Analysis of ChIP-seq) identifies regions of significant read enrichment (peaks) from ChIP-seq, ATAC-seq, CUT&RUN, and CUT&TAG experiments. It models the fragment length distribution from paired-end data or estimates it from mono-nucleosomal read shifting in single-end data, then applies a Poisson model to identify fold-enrichment over an input/IgG control. MACS3 produces BED-format narrowPeak (for transcription factors) or broadPeak (for histone marks) files with signal and q-value tracks for visualization in IGV or UCSC Genome Browser. ## When to Use - Calling transcription factor binding peaks from ChIP-seq experiments (use `--nomodel --extsize 200` or let MACS3 estimate fragment length) - Identifying open chromatin regions from ATAC-seq experiments (use `--nomodel --shift -100 --extsize 200 -f BAMPE`) - Calling broad histone modification peaks (H3K27me3, H3K9me3, H3K36me3) with `--broad` - Generating peak signal tracks (bedGraph/bigWig) for genome browser visualization with `-B --SPMR` - Performing differential binding analysis: MACS3 peaks as input to DiffBind or DESeq2 …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/macs3-peak-calling@sha256:eafae23ab84477b7The line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_wgwzge64kkze7rdh)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Feb 18, 2026 and Sep 29, 2026, about one every 56 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 13,892 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 13,941 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 11,826 B | A | view · diff |
| git:20260414.65bebbb | 2026-04-14 | 65bebbb | 11,951 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 11,633 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (13892 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_wgwzge64kkze7rdh GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/macs3-peak-calling GET https://markdownregistry.com/api/v1/blob/eafae23ab84477b773992887454a36b25b54c339e38df6a0ffe39b5ad13566e9
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.