bio-chipseq-differential-binding SKILL.md skillA
bio-chipseq-differential-binding from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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- git:20260821.2d1b678, committed Aug 21, 2026
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- MIT
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in…
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What the file says
## Version Compatibility
Reference examples tested with: DiffBind 3.20+, DESeq2 1.42+, edgeR 4.0+, csaw 1.36+, PyDESeq2 0.5+, NormR 1.28+, MAnorm2 1.2+, ChIPseqSpikeInFree 1.6+.
DiffBind 3.0+ changed defaults: `summits=200` (was FALSE), `dba.normalize()` now required, blacklist filtering on by default, full library size normalization replaces reads-in-peaks. Always run `packageVersion('DiffBind')` and inspect `dba.normalize(obj, bRetrieve=TRUE)` to confirm what was applied.
# Differential ChIP-seq Binding
**"Compare protein-DNA binding between experimental conditions"** -> Identify regions where IP signal changes significantly, accounting for sequencing depth, composition bias, trended biases, and global shifts that confound naive normalization.
- R (BAM + peaks): `DiffBind::dba()` -> `dba.count()` -> `dba.normalize()` -> `dba.analyze()`
- R (count matrix): `DESeq2::DESeq()` or `edgeR::glmQLFTest()` on a peaks-by-samples matrix
- R (windows-based, global-shift-robust): `csaw::windowCounts()` -> `csaw::normFactors()` -> `edgeR::glmQLFTest()`
- R (control-aware): `normr::diffR(chip1.bam, chip2.bam, genome)` joint binomial mixture
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How to install
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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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