omics-scatac
Automated workflow for scATAC-seq analysis, covering QC, clustering, motif activity, and peak linkage.
Install
mkdir -p .claude/skills/omics-scatac && curl -L -o skill.zip "https://agentskills.codes/api/skills/download/14419" && unzip -o skill.zip -d .claude/skills/omics-scatac && rm skill.zipInstalls to .claude/skills/omics-scatac
Activation
This is the description your AI agent reads to decide when to run this skill — the better it matches your request, the more reliably it fires.
Single-cell ATAC-seq — fragment import, ATAC QC (TSS / fragment-size / FRiP / doublets), feature matrix (tiles / MACS3 peaks), spectral (LSI) clustering, motif activity (chromVAR), gene activity, peak–gene linkage, scRNA label transfer.Key capabilities
- →Import fragments into cell×feature matrix
- →Perform ATAC QC (TSS, fragment size, FRiP, doublets)
- →Generate feature matrices (tiles/peaks)
- →Call peaks using MACS3 per cluster
- →Perform spectral (LSI) embedding and Leiden clustering
- →Calculate gene activity scores
How it works
The skill processes single-cell ATAC-seq data by importing fragments, performing quality control, and generating feature matrices. It then applies spectral embedding for clustering and calculates gene activity scores.
Inputs & outputs
When to use omics-scatac
- →Importing and QC-ing fragment files
- →Calling peaks with MACS3
- →Analyzing gene activity and peak linkages
About omics-scatac
This skill manages single-cell ATAC-seq pipelines, including fragment import, QC, and peak calling. It automates spectral clustering, chromVAR motif analysis, and scRNA label transfer.
Single-cell ATAC-seq — fragment import, ATAC QC (TSS / fragment-size / FRiP / doublets), feature matrix (tiles / MACS3 peaks), spectral (LSI) clustering, motif activity (chromVAR), gene activity, peak–gene linkage, scRNA label transfer.
When not to use it
- →When inferring GRN from accessibility alone
- →When using PCA instead of spectral embedding for ATAC data
- →When expecting gene activity scores to be measured expression
Prerequisites
Limitations
- →GRN inference is not a pure-scATAC step
- →Accessibility ≠ expression
- →Distance ≠ regulation
How it compares
This skill provides a structured workflow for scATAC-seq analysis, including specialized QC and embedding methods for sparse ATAC data, which differs from generic single-cell analysis pipelines.
Compared to similar skills
omics-scatac side by side with the closest alternatives in the catalog.
| Skill | Installs | Updated | Safety | Difficulty |
|---|---|---|---|---|
| omics-scatac (this skill) | 0 | 1mo | No flags | Advanced |
| quant-analyst | 103 | 2mo | No flags | Advanced |
| umap-learn | 6 | 2mo | Review | Intermediate |
| embedding-strategies | 8 | 2mo | No flags | Intermediate |
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Example prompts that trigger this skill in your AI assistant.
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