bio-chipseq-chromatin-state-segmentation SKILL.md skillA
bio-chipseq-chromatin-state-segmentation from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-chipseq-chromatin-state-segmentation@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-chip-seq-chromatin-state-segmentation/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,714 bytes
- Repository stars
- 662
- License
- MIT
Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection…
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
## Version Compatibility Reference examples tested with: ChromHMM 1.27+, Segway 3.0+, EpiSegMix 1.0+, EpiLogos (Meuleman lab), IDEAS 1.20+, samtools 1.19+, bedtools 2.31+. ChromHMM requires Java 8+; runs as `java -mx<MEMORY> -jar ChromHMM.jar <command>`. # Chromatin State Segmentation **"Integrate multiple histone modification ChIP-seq tracks into chromatin states"** -> Learn a small set of recurring combinatorial patterns of histone marks (active promoter, active enhancer, poised enhancer, polycomb-repressed, heterochromatic, transcribed, etc.) and segment the genome by which state each region belongs to. Output: per-state genomic intervals, state-by-mark emission matrix, and state-state transition matrix. - CLI (canonical): ChromHMM `BinarizeBam` -> `LearnModel` -> `OverlapEnrichment` / `NeighborhoodEnrichment` - CLI (continuous signal): Segway `train` -> `posterior` -> `annotate` - CLI (flexible distributions): EpiSegMix (2024) - Visualization across biosamples: EpiLogos (Meuleman lab) - Cell-type-aware joint: IDEAS …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-chromatin-state-segmentation@sha256:76d15b3def44ad01The line at the top of this page pins the label git:20260821.2d1b678, 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_ibnbkquyggwbdrji)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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 (15714 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
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ibnbkquyggwbdrji GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-chromatin-state-segmentation GET https://markdownregistry.com/api/v1/blob/76d15b3def44ad01bfaec6c30f0b94adf22688d5dee4d9c942cdd300efe3f013
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.