bio-atac-seq-co-accessibility SKILL.md skillA
bio-atac-seq-co-accessibility 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-atac-seq-co-accessibility@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
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skills/bioskills/bio-atac-seq-co-accessibility/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- 662
- License
- MIT
Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.
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: Cicero 1.20+, monocle3 1.3+, ArchR 1.0.2+, SCENIC+ 1.0+, pycisTopic 1.0+, Signac 1.13+, GenomicRanges 1.54+, GenomicInteractions 1.36+, BSgenome.Hsapiens.UCSC.hg38 1.4+.
Verify before use:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- Python: `pip show <package>` then `help(module.function)` to check signatures
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Co-accessibility (cis-Regulatory Linkage)
**"Which enhancers connect to which promoters in my scATAC data?"** -> Use cell-to-cell variability in joint accessibility of nearby peaks to infer cis-regulatory connections without explicit RNA expression. Output is a peak-pair graph with co-accessibility scores; thresholding produces enhancer-gene candidate pairs.
- R: `cicero::run_cicero(input_cds, genomic_coords)` -> peak-pair connection scores
- R: `ArchR::addCoAccessibility(proj)` -> ArchR-internal Cicero wrapper
- Python: `pycisTopic` + `SCENIC+` for network-level inference combining ATAC + RNA + motifs
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-co-accessibility@sha256:64947c6bb46c75b7The 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_224vfdiw4h4gyswk)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_224vfdiw4h4gyswk GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-co-accessibility GET https://markdownregistry.com/api/v1/blob/64947c6bb46c75b7b66dde281ddab2679ee438b1ea077c8f10568eab0933de15
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.