bio-chipseq-peak-calling SKILL.md skillA
bio-chipseq-peak-calling 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-calling@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-calling/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 20,301 bytes
- Repository stars
- 662
- License
- MIT
Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs…
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: MACS3 3.0.4+, MACS2 2.2.9+, HOMER 4.11+, SPP 1.16+, samtools 1.19+, bedtools 2.31+, IDR 2.0.4+. Before running, verify versions: `<tool> --version` and `<tool> --help` to confirm flags. If a flag is missing, check the changelog — MACS2->MACS3 is API-compatible for `callpeak` but `predictd`, `bdgpeakcall`, and `hmmratac` differ. # ChIP-seq Peak Calling **"Identify protein-DNA binding sites from ChIP-seq alignments"** -> Detect statistically enriched genomic regions by comparing IP signal to input control (or genomic background), with peak shape (narrow/broad) determined by target biology (TF vs histone mark). - CLI (ENCODE TF default): `macs2 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --keep-dup all -p 1e-2` - CLI (ENCODE histone default): same with `--broad --broad-cutoff 0.1` for H3K27me3, H3K9me3, H3K36me3 - CLI (alternative): `macs3 callpeak ...` (API-identical, active development), HOMER `findPeaks tags/ -style histone -i input_tags/`, SPP via phantompeakqualtools wrapper …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-peak-calling@sha256:2a9380888e608c2dThe 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.
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Versions
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
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