bio-atac-seq-atac-qc SKILL.md skillA
bio-atac-seq-atac-qc from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-qc@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bio-atac-seq-atac-qc/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
- Size
- 8,921 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility
Reference examples tested with: bedtools 2.31+, deepTools 3.5+, numpy 1.26+, pandas 2.2+, picard 3.1+, pyBigWig 0.3+, pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- 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 ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# ATAC-seq Quality Control
**"Check the quality of my ATAC-seq library"** → Evaluate fragment size distribution (nucleosome periodicity), TSS enrichment, FRiP, and library complexity to assess chromatin accessibility experiment quality.
- CLI: `deeptools bamPEFragmentSize`, `picard CollectInsertSizeMetrics`
- Python: `pysam` for custom fragment analysis
## Fragment Size Distribution
**Goal:** Assess ATAC-seq library quality by visualizing the characteristic nucleosome periodicity in fragment sizes.
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-qc@sha256:b39fbdfee242850eThe line at the top of this page pins the label git:20260517.81511a7, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_jalwzecyq4x7c5ui)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
Audit of the latest version
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- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
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- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jalwzecyq4x7c5ui GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-atac-qc GET https://markdownregistry.com/api/v1/blob/b39fbdfee242850e9b3feda05a0e0a54dc1cf3920a047257cdee9d37e29b83f2
Your AI assistant 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.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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