bio-atac-seq-allele-specific-accessibility SKILL.md skillA
bio-atac-seq-allele-specific-accessibility 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-allele-specific-accessibility@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/allele-specific-accessibility/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260719.44d7640, committed Jul 19, 2026
- First version recorded
- May 17, 2026
- Size
- 17,049 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.
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: WASP 0.3.4+, GATK 4.4+, RASQUAL 1.1+, samtools 1.19+, bcftools 1.19+, vcftools 0.1.16+, plink 2.00+, MatrixEQTL 2.3+, QuASAR 0.1+, bowtie2 2.5+, bwa-mem2 2.2.1+, scipy 1.11+ (false_discovery_control), pandas 2+, pybedtools 0.10+.
Verify before use:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
# Allele-Specific Accessibility
**"Does this heterozygous SNP affect chromatin accessibility on its allele?"** -> Count ATAC reads supporting reference vs alternative allele at heterozygous sites in the same individual; significant deviation from 50:50 indicates cis-regulatory effect. Requires careful handling of reference-allele mapping bias (WASP filtering) and within-individual binomial testing.
- CLI: `WASP` (Geijn 2015) for de-biased reference mapping
- CLI: `gatk ASEReadCounter` for allele-specific count tables
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-allele-specific-accessibility@sha256:516426242161aa11The 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_5aakxglb6hwlgvgw)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 17, 2026 and Jul 19, 2026, about one every 31 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260719.44d7640 latest | 2026-07-19 | 44d7640 | 17,049 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 16,512 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 16,478 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 (17049 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_5aakxglb6hwlgvgw GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-allele-specific-accessibility GET https://markdownregistry.com/api/v1/blob/516426242161aa119dfef2337b7cd8cc5ac0b83d9b66c48f69e6f99f67862e39
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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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