bio-atac-seq-enhancer-gene-linking SKILL.md skillA
bio-atac-seq-enhancer-gene-linking 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-enhancer-gene-linking@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-atac-seq-enhancer-gene-linking/SKILL.md- Versions recorded
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- git:20260821.2d1b678, committed Aug 21, 2026
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- MIT
Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.
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: ABC-Enhancer-Gene-Prediction 0.2.2+ (Engreitz lab), ENCODE-rE2G v1.0+ (EngreitzLab), Cicero 1.20+, GenomicInteractions 1.36+, FitHiChIP 9.1+, HiC-Pro 3.1+, FAN-C 0.9+, MACS3 3.0+, samtools 1.19+, bedtools 2.31+.
Verify before use:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
- 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.
# Enhancer-Gene Linking
**"Which gene does this distal accessible region regulate?"** -> Predict the enhancer's target gene using a model that combines accessibility activity, 3D contact frequency, and (optionally) sequence-based chromatin predictions. Output is a per-(enhancer, gene) score that can be thresholded for high-confidence calls.
- CLI: ABC pipeline (`run.neighborhoods.py`, `predict.py` from Engreitz lab)
- CLI: ENCODE-rE2G (Snakemake-based; ENCODE 4 enhancer-gene standard)
- R: Cicero (ATAC-only; covered in atac-seq/co-accessibility)
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-enhancer-gene-linking@sha256:cf5fb75a5d7180c3The 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_qgc3dk7k7scvx4q5)
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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_qgc3dk7k7scvx4q5 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-enhancer-gene-linking GET https://markdownregistry.com/api/v1/blob/cf5fb75a5d7180c302e9973237d52e789897af34113b91830cc2711be364c8e8
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