bio-atac-seq-deep-learning-atac SKILL.md skillA
bio-atac-seq-deep-learning-atac 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-deep-learning-atac@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-atac-seq-deep-learning-atac/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,082 bytes
- Repository stars
- 662
- License
- MIT
Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.
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: chrombpnet 0.1.7+, bpnet-lite 0.6+ (github.com/jmschrei/bpnet-lite), scBasset 0.1.0+ (basenji2 fork), tangermeme 0.1+, tfmodisco-lite 2.2+, DeepLIFT 0.6+, captum 0.7+, tensorflow 2.13+, pytorch 2.1+, kipoi 0.8+. Verify before use: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws unexpected errors, introspect the installed package and adapt rather than retrying. Deep-learning tooling evolves rapidly; method papers post 2023 may have superseded reference implementations. # Sequence-Based Deep Learning for ATAC-seq **"Score the effect of a GWAS SNP on chromatin accessibility"** -> Train (or use pre-trained) sequence-to-accessibility CNNs that take 1-5 kb DNA windows and predict per-base Tn5 cleavage profiles. Outputs include: bias-corrected accessibility, single-base mutation effect predictions, and DeepLIFT contribution scores convertible to motifs via TF-MoDISco. - CLI: `chrombpnet pipeline --bigwig signal.bw --bigwig-bias bias.bw ...` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-deep-learning-atac@sha256:b588803cc1ab6cf3The 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_jdvf5ir7zilqpoek)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No instruction hidden inside an HTML comment
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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_jdvf5ir7zilqpoek GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-deep-learning-atac GET https://markdownregistry.com/api/v1/blob/b588803cc1ab6cf32a71425e864a304123a05e299bbdcfa8a78c3d344727d495
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.