bio-chipseq-allele-specific-binding SKILL.md skillA
bio-chipseq-allele-specific-binding 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-allele-specific-binding@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-allele-specific-binding/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,675 bytes
- Repository stars
- 638
- License
- MIT
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying…
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: WASP 0.3.4+, RASQUAL 1.1+, BaalChIP 1.30+ (Bioconductor), AlleleSeq 2.0+, samtools 1.19+, bcftools 1.19+, GATK 4.5+, pysam 0.22+. # Allele-Specific Binding (ASB) **"Identify variants that affect transcription factor or histone modification binding in cis"** -> Compare ChIP-seq read counts at the reference and alternate alleles of heterozygous variants in a single sample. Differential read counts (ALT vs REF at hetSNPs in peaks) reveal allele-specific binding. - CLI (mandatory bias filter): WASP `mapping pipeline` to remove reference-allele mapping bias - CLI (joint association): RASQUAL for cis-QTL + ASB (genotype VCF piped in via tabix) - R (Bayesian beta-binomial): BaalChIP with copy-number-aware overdispersion - CLI (personalized genome): AlleleSeq with phased diploid genome - Statistical test: beta-binomial likelihood ratio or chi-squared on count tables …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-allele-specific-binding@sha256:102bcc9d9ab421d7The 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_6mfqbet25bjrqlyy)
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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 credential-shaped string
- pass: No instruction to send local credentials anywhere
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- pass: No script tag
Source
pku-yuangroup/openai4s · 638 stars · license MIT · pushed 2026-10-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_6mfqbet25bjrqlyy GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-allele-specific-binding GET https://markdownregistry.com/api/v1/blob/102bcc9d9ab421d7b9af154743ebbc16117065c5f0a4d5b55a6e04187f8127d8
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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.
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