bio-methylation-array-preprocessing SKILL.md skillA
bio-methylation-array-preprocessing 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-preprocessing@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-preprocessing/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260614.5d4591c, committed Jun 14, 2026
- Size
- 18,091 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Turns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi (RGChannelSet -> MethylSet -> GenomicRatioSet). Covers Type I vs Type II probe chemistry and why raw Type II beta is compressed, the signal-to-beta math (beta = M/(M+U+100)) and M-value logit, detection-p / pOOBAH masking including the out-of-band deletion-artifact catch, dye-bias correction, and the normalization decision…
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: sesame 1.20+, minfi 1.48+, ChAMP 2.32+, wateRmelon 2.8+.
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 and GENOME BUILD are versions that matter as much as the package. EPICv2 REQUIRES sesame (mainstream minfi does not auto-detect it and returns "Unknown"); the manifest/annotation packages are array-version- and genome-build-specific (450K and EPICv1 are hg19; EPICv2 is hg38-native). sesame pulls platform/address data from its own hub, so `sesameDataCache()` must run once before processing. Record the array (450K/EPIC/EPICv2) and the genome build in any output, the way a sequencing run records its reference.
# Array Preprocessing
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-methylation-array-preprocessing@sha256:b21c17d47139d332The 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_qma6tmtvnk3omm3g)
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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 (18091 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_qma6tmtvnk3omm3g GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-methylation-array-preprocessing GET https://markdownregistry.com/api/v1/blob/b21c17d47139d3328c6675ded7e49238791dd55d9119dde583a74b41468d554c
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.