bio-chipseq-super-enhancers SKILL.md skillA
bio-chipseq-super-enhancers 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-super-enhancers@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-super-enhancers/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,712 bytes
- Repository stars
- 662
- License
- MIT
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers…
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: ROSE (stjude/ROSE, 2018+), ROSE2 (linlabbcm/rose2, 2021+), LILY (BoevaLab/LILY, 2020+), HOMER 4.11+, samtools 1.19+, bedtools 2.31+, GenomicRanges 1.54+. The original Young-lab ROSE is Python 2; ROSE2 (linlabbcm/rose2) and the stjude/ROSE fork are the Python-3 implementations with the same algorithm. For hg38 data use stjude/ROSE (`python ROSE_main.py`, whose genomeDict includes HG38); rose2's released genomeDict covers only HG18/HG19/MM8/MM9/MM10/RN4/RN6, so `rose2 -g HG38` fails. LILY (Boeva 2017) is a refactored implementation with input-control background subtraction for low-quality H3K27ac data. # Super-Enhancer Calling **"Identify super-enhancers driving cell identity / cancer biology"** -> Stitch nearby active enhancer peaks (H3K27ac, MED1, or BRD4) within a stitching window, exclude proximal-promoter signal, rank by total signal, find the hockey-stick inflection point where signal sharply increases, and classify all stitched regions above the inflection as super-enhancers. - CLI (stjude/ROSE, Python 3): `python ROSE_main.py -g HG38 -i peaks.gff -r h3k27ac.bam -c input.bam -s 12500 -t 2500 -o rose_out/` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-super-enhancers@sha256:acf240637c9895abThe 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_nxysdooti2scpaw3)
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 (16712 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_nxysdooti2scpaw3 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-super-enhancers GET https://markdownregistry.com/api/v1/blob/acf240637c9895ab3c701bdcd82ff6c644888f99fe8eb1c7dbd28e53186385f4
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.
More from pku-yuangroup/openai4s
Every file in pku-yuangroup/openai4s