bio-atac-seq-differential-accessibility skillA
bio-atac-seq-differential-accessibility is agent-read markdown (skill) from pku-yuangroup/openai4s: Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility
Reference examples tested with: DiffBind 3.12+, DESeq2 1.42+, edgeR 4.0+, csaw 1.36+, limma 3.58+, GenomicRanges 1.54+, ChIPseeker 1.38+, Subread 2.0+ (featureCounts), sva 3.50+, RUVSeq 1.36+.
Before using code patterns, verify installed versions match:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Differential Accessibility
**"Find chromatin regions that change accessibility between my conditions"** -> Build a sample-by-region count matrix, normalize for library size and chromatin compaction, fit a generalized linear model (negative-binomial), and extract regions with significant accessibility change.
- R (consensus-peak workflow): `DiffBind` -> count -> normalize -> contrast -> analyze
- R (window-based, no peak set): `csaw::windowCounts` + `filterWindowsGlobal` + edgeR QL F-test
- R (existing peak-count matrix): `DESeq2` or `edgeR` directly on `featureCounts` output
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-differential-accessibility@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-differential-accessibility@sha256:914abeb9fe30d955Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_6w3qfjvhc5ijowdr)
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Versions
Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_6w3qfjvhc5ijowdr GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-differential-accessibility GET https://markdownregistry.com/api/v1/blob/914abeb9fe30d9554b7f3955bc5076a770057c05af3d69a1f645a7ca9503f7cf
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