bio-atac-seq-co-accessibility skillA
bio-atac-seq-co-accessibility is agent-read markdown (skill) from pku-yuangroup/openai4s: Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth..
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What the file says
## Version Compatibility
Reference examples tested with: Cicero 1.20+, monocle3 1.3+, ArchR 1.0.2+, SCENIC+ 1.0+, pycisTopic 1.0+, Signac 1.13+, GenomicRanges 1.54+, GenomicInteractions 1.36+, BSgenome.Hsapiens.UCSC.hg38 1.4+.
Verify before use:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- Python: `pip show <package>` then `help(module.function)` to check signatures
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Co-accessibility (cis-Regulatory Linkage)
**"Which enhancers connect to which promoters in my scATAC data?"** -> Use cell-to-cell variability in joint accessibility of nearby peaks to infer cis-regulatory connections without explicit RNA expression. Output is a peak-pair graph with co-accessibility scores; thresholding produces enhancer-gene candidate pairs.
- R: `cicero::run_cicero(input_cds, genomic_coords)` -> peak-pair connection scores
- R: `ArchR::addCoAccessibility(proj)` -> ArchR-internal Cicero wrapper
- Python: `pycisTopic` + `SCENIC+` for network-level inference combining ATAC + RNA + motifs
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-co-accessibility@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-co-accessibility@sha256:64947c6bb46c75b7Pin 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_224vfdiw4h4gyswk)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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