atac-seq
ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
npx skills add BioTender-max/awesome-bio-agent-skills --skill atac-seq --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ATAC Seq ## Version Compatibility Reference examples assume: - `macs3` 3.0+ - `samtools` 1.18+ - `deepTools` 3.5+ Verify the runtime first: - CLI: `macs3 --version`, `samtools --version`, `bamCoverage --version` ## Overview Use this skill when the user needs: - bulk ATAC-seq QC - peak calling - accessibility counting - differential accessibility - motif deviation or footprint follow-up ## When To Use This Skill - the task is bulk ATAC-seq rather than ChIP-seq - TSS enrichment, fragment periodicity, or FRiP need review - the output should include peaks, counts, and downstream accessibility summaries ## Quick Route - paired-end bulk ATAC: use `BAMPE` - call peaks without control using ATAC-specific settings - if TSS enrichment is poor, stop and flag data quality before interpretation ## Progressive Disclosure - Read [technical_reference.md](technical_reference.md) for QC gates and assay-specific caveats. - Read [commands_and_thresholds.md](commands_and_thresholds.md) for peak-calling commands, thresholds, and output conventions. ## Prerequisites | Check | Guidance | |---|---:| | uniquely mapped reads | `>= 20M` preferred for strong bulk ATAC | | TSS enrichment | `> 7` acceptable, `
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Prerequisites
- Expected Inputs
- Expected Outputs
- Starter Pattern
- Key Parameters
- Workflow
- 1. Validate assay QC
- 2. Call peaks with ATAC-specific settings
- 3. Build a consensus peak matrix
macs3 callpeak \
What does the atac-seq skill do?
ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill atac-seq --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.