bio-methylation-array-preprocessing
PKU-YuanGroup/OpenAI4STurns raw Illumina Infinium methylation BeadChip IDATs (450K, EPIC, EPICv2) into a defensible beta/M matrix with sesame (openSesame/SigDF) or minfi…
Scores out of 100 · grade B+
2026-08-22Works
40% of the score92/100
- Frontmatter name `bio-methylation-array-preprocessing` does not match its directory `bio-methylation-analysis-array-preprocessing`.
Maintained
25% of the score100/100
- no commits in the last 12 weeks
Adopted
20% of the score35/100
- 335 stars on the source repo.
Documented
15% of the score82/100
- 2,378 words with worked examples.
- Ships 2 bundled files.
Install
npx skills add PKU-YuanGroup/OpenAI4S/bio-methylation-array-preprocessingWhat the check found
| Finding | What it means |
|---|---|
| Name mismatch | The frontmatter name and the directory name disagree. |
What it says it does
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 (noob, funnorm, quantile, SWAN, BMIQ, dasen, sesame QCDPB). Use when reading IDATs, choosing a normalization for a 450K/EPIC/EPICv2 cohort, deciding beta vs M, masking failed probes, or producing the corrected matrix before testing. For probe/sample filtering, EPICv2 replicate collapse, and sample-identity QC see array-qc-filtering; for native long-read 5mC see long-read-sequencing/nanopore-methylation (a different platform).
Also in PKU-YuanGroup/OpenAI4S
| Artifact | Score | What the check found | Type | Reach | Last commit |
|---|---|---|---|---|---|
| bio-atac-seq-allele-specific-accessibilityPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-atac-peak-callingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-consensus-peaksetPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-deep-learning-atacPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-footprintingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-causal-genomics-effector-gene-prioritizationPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today |
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