bio-chipseq-chip-deep-learning SKILL.md skillA
bio-chipseq-chip-deep-learning 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-chip-deep-learning@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-chip-deep-learning/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,319 bytes
- Repository stars
- 662
- License
- MIT
Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for…
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 0.0.23+, TF-MoDISco-lite 2.0+, EnFormer (Avsec lab Colab + DeepMind release), tensorflow 2.13+, pytorch 2.0+, JASPAR 2026 deep-learning collection (released 2025). # Deep Learning for ChIP-seq **"Predict TF binding from sequence and quantify variant effects on binding"** -> Train base-resolution convolutional / transformer models on ChIP-seq / ChIP-nexus / CUT&RUN profiles; predict reference and alternate-allele binding profiles for variants; extract motif syntax via TF-MoDISco from sequence-attribution scores. - Python (modern): chrombpnet (bias-factorized; ATAC/DNase/ChIP) - Python (canonical TF ChIP): BPNet (originally for ChIP-nexus; soft motif syntax) - Python (long-range): EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input window, ~100 kb effective receptive field; tissue-aggregated training) - Python (multi-task): DeepSEA (Zhou 2015; older but still used) - Precomputed: JASPAR 2026 Deep Learning collection (1259 BPNet ChIP models from ENCODE; 240 TFs) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-chip-deep-learning@sha256:121b566b7200cde2The 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_qmg2kgsqsrjlznnr)
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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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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qmg2kgsqsrjlznnr GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-chip-deep-learning GET https://markdownregistry.com/api/v1/blob/121b566b7200cde29ba867c3aa72b43b689fb5988722a36d016fba6956a464fa
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.