bio-methylation-array-qc-filtering SKILL.md skillA
bio-methylation-array-qc-filtering 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-methylation-array-qc-filtering@git:20260614.5d4591cPins git:20260614.5d4591c 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/array-qc-filtering/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260614.5d4591c, committed Jun 14, 2026
- Size
- 19,144 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions…
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: minfi 1.48+, sesame 1.20+, maxprobes 0.0.2+, ChAMP 2.32+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
The ARRAY VERSION is the version that matters most here. Cross-reactive probe lists, SNP-overlap annotation, the manifest, and the genome build are all array-version-specific. Record whether the data is 450K (hg19), EPIC v1 (hg19), or EPIC v2 (hg38), and which annotation package supplies the probe metadata (`IlluminaHumanMethylation450kanno.ilmn12.hg19`, `...EPICanno.ilm10b4.hg19`, `...EPICv2anno.20a1.hg38`). EPICv2 carries ~5,100 replicate probes (2-10 designs per locus) and is hg38-native; both facts break naive cross-version merges if ignored.
# Array QC and Filtering
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-methylation-array-qc-filtering@sha256:ce95ec88d5b84608The line at the top of this page pins the label git:20260614.5d4591c, 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_ektuxzkjzuzdg72k)
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Versions
The registry has recorded 1 version of this file, committed on Jun 14, 2026.
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 (19144 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_ektuxzkjzuzdg72k GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-methylation-array-qc-filtering GET https://markdownregistry.com/api/v1/blob/ce95ec88d5b84608fc1293ac9e66d674c248d2a55380601dd938a9f7e961f218
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.