bio-chipseq-spike-in-normalization SKILL.md skillA
bio-chipseq-spike-in-normalization 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-spike-in-normalization@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-spike-in-normalization/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,975 bytes
- Repository stars
- 662
- License
- MIT
Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected…
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: DiffBind 3.20+, DESeq2 1.42+, edgeR 4.0+, csaw 1.36+, ChIPseqSpikeInFree 1.6+, SpikChIP 1.0+, SpikeFlow (NAR Genom Bioinform 2024), samtools 1.19+, bowtie2 2.5+. # ChIP-seq Spike-In Normalization **"Account for global signal changes that defeat standard normalization"** -> Add exogenous reference chromatin (Drosophila for human/mouse ChIP-Rx; E. coli carryover for CUT&RUN/CUT&Tag) at fixed concentration BEFORE IP, derive scaling factors from spike-in read counts, and apply at the read or size-factor level (never to peak counts) to enable quantitative cross-condition comparison. - CLI: align reads to combined target + spike genome; count spike reads via `samtools view -c` - R (DiffBind integration): `dba.normalize(obj, spikein = TRUE)` - R (DESeq2 / edgeR): `sizeFactors(dds) <- 1 / scale_factors` (note inverse) - CLI (deepTools tracks): `bamCoverage --scaleFactor <derived>` (use alone; `--normalizeUsing` compounds with it) - Wrapper: SpikeFlow (Snakemake; 2024) automates end-to-end - Post-hoc detection: ChIPseqSpikeInFree (when no spike-in was added) …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-spike-in-normalization@sha256:985abd0572e15457The 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_arr5aofzwt7x2jmk)
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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
GET https://markdownregistry.com/api/v1/artifacts/art_arr5aofzwt7x2jmk GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-chipseq-spike-in-normalization GET https://markdownregistry.com/api/v1/blob/985abd0572e154576ee29916334cac4cbe70eb6db6c36aa92bcee9e97cfd9665
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