bio-chipseq-peak-annotation SKILL.md skillA
bio-chipseq-peak-annotation 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-peak-annotation@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-peak-annotation/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 18,668 bytes
- Repository stars
- 662
- License
- MIT
Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window…
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: ChIPseeker 1.38+, GenomicFeatures 1.54+, rtracklayer 1.62+, HOMER 4.11+, rGREAT 2.4+, chipenrich 2.26+, pyranges 0.0.129+, pandas 2.2+. ENCODE cCRE registry expanded to 2.37M human and 967k mouse elements (Moore JE et al 2026 Nature). SCREEN web app at screen.encodeproject.org provides browser access; ENCODE provides bed files for batch annotation. # Peak Annotation **"What genes and regulatory elements do my peaks correspond to?"** -> Assign each peak to a genomic feature (promoter, exon, intron, intergenic), its target gene (via nearest-TSS or host-gene), and where applicable an ENCODE cCRE class (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3). - R (gene-feature): `ChIPseeker::annotatePeak(peaks, TxDb=txdb)` - CLI (gene-feature): `annotatePeaks.pl peaks.bed hg38 -gtf annotation.gtf` - Python (custom): pyranges + pandas - R (cCRE classification): intersect peaks with ENCODE cCRE BED from SCREEN - R (gene-set enrichment): `rGREAT::great()` or `chipenrich::chipenrich()` …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-peak-annotation@sha256:31ae7a0861584979The 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_pahnuwthmlo2jvfq)
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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 to send local credentials anywhere
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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