bio-atac-seq-single-cell-atac skillA
bio-atac-seq-single-cell-atac is agent-read markdown (skill) from pku-yuangroup/openai4s: Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster..
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: Cell Ranger ATAC 2.1+, Signac 1.13+, Seurat 5.0+, ArchR 1.0.2+, SnapATAC2 2.8+, AMULET 1.1+, scDblFinder 1.16+, scater 1.30+, scvi-tools 1.1+, GenomicRanges 1.54+, JASPAR2024 0.99+, BSgenome.Hsapiens.UCSC.hg38 1.4+, EnsDb.Hsapiens.v86 2.99+, MACS3 3.0+. SnapATAC2 2.8+ uses `pp.import_fragments`; older 2.5-2.7 used `pp.import_data` (renamed/removed in 2.9).
Verify before use:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Single-Cell ATAC-seq
**"Process my 10X scATAC data from cellranger output"** -> Build a per-cell fragment matrix, compute per-cell QC, dimensionality reduction (TF-IDF + LSI / spectral / autoencoder), cluster, call cluster-level pseudobulk peaks, annotate cell types via gene-activity scores, and integrate with paired scRNA-seq if Multiome.
- R: `Signac::CreateChromatinAssay()` -> `Seurat` workflow (TF-IDF + SVD + UMAP + Leiden)
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-single-cell-atac@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-single-cell-atac@sha256:96bb386937c4c305Pin 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_j7wow4cyb2xgpsa7)
1 badge views in 30 days
Versions
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (24123 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_j7wow4cyb2xgpsa7 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-single-cell-atac GET https://markdownregistry.com/api/v1/blob/96bb386937c4c305e82251e53fed186a0fbe74d3375bb556b7cb6f2680f3f8fb
Your agent does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.