bio-atac-seq-motif-deviation skillA
bio-atac-seq-motif-deviation is agent-read markdown (skill) from pku-yuangroup/openai4s: Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting..
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What the file says
## Version Compatibility
Reference examples tested with: chromVAR 1.24+, motifmatchr 1.24+, JASPAR2024 0.99+, TFBSTools 1.40+, BSgenome.Hsapiens.UCSC.hg38 1.4+, SummarizedExperiment 1.32+, limma 3.58+, ggplot2 3.5+, Matrix 1.6+, ArchR 1.0.2+, Signac 1.13+.
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# Motif Deviation (chromVAR)
**"Which TF motifs explain accessibility variation across my samples or cells?"** -> Compute per-sample (or per-cell) deviation z-scores: how many standard deviations above expectation each TF motif's accessibility falls, controlling for GC content and overall accessibility via matched background peak sets.
- R: `chromVAR::computeDeviations(counts, motifs)` -> per-sample z-scores
- R: `chromVAR::computeVariability(dev)` -> per-motif variance ranking
- Single-cell alternative: `Signac::RunChromVAR()` (wrapper with matched defaults) or `ArchR::addDeviationsMatrix()`
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How to install
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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