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:20260719.44d7640Pins git:20260719.44d7640 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/atac-qc/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260719.44d7640, committed Jul 19, 2026
- First version recorded
- May 17, 2026
- Size
- 20,022 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.
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: deepTools 3.5+, Picard 3.1+, samtools 1.19+, bedtools 2.31+, ATACseqQC 1.26+, pysam 0.22+, pyBigWig 0.3+, numpy 1.26+, pandas 2.2+, MultiQC 1.21+.
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.
# ATAC-seq Quality Control
**"Does my ATAC library pass ENCODE quality criteria?"** -> Compute the seven canonical metrics (depth, alignment rate, mitochondrial fraction, library complexity, fragment-size periodicity, TSS enrichment, FRiP) and compare against ENCODE 4 thresholds, then diagnose failures.
- CLI: `picard CollectInsertSizeMetrics`, `samtools flagstat`, `samtools idxstats`
- CLI: `deeptools plotFingerprint`, `computeMatrix reference-point` + `plotProfile`
- R: `ATACseqQC::TSSEscore`, `ATACseqQC::fragSizeDist`, `ATACseqQC::PTscore`
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-atac-qc@sha256:ac0ae172d8d6d4b5The line at the top of this page pins the label git:20260719.44d7640, 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_545imycqbcar3wqa)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and Jul 19, 2026, about one every 63 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260719.44d7640 latest | 2026-07-19 | 44d7640 | 20,022 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 19,497 B | A | view |
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 (20022 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_545imycqbcar3wqa GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-atac-qc GET https://markdownregistry.com/api/v1/blob/ac0ae172d8d6d4b5c03ac01ab19f1cf8c6c544c4acc6187d2670184e3f3aa1b0
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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