bio-expression-matrix-metadata-joins
lilinji/GeneTind-Life-SkillsAligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE…
Scores out of 100 · grade B+
2026-08-22Works
40% of the score100/100
- Loads cleanly: valid frontmatter, required fields present, no dangling references.
Maintained
25% of the score94/100
- no commits in the last 12 weeks
- no license file
Adopted
20% of the score13/100
- 8 stars on the source repo.
Documented
15% of the score91/100
- 3,326 words with worked examples.
- Ships 2 bundled files.
Install
npx skills add lilinji/GeneTind-Life-Skills/bio-expression-matrix-metadata-joinsWhat the check found
| Finding | What it means |
|---|---|
| No license | The repository ships no license file, so the reuse terms are unclear. |
What it says it does
Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.
Also in lilinji/GeneTind-Life-Skills
| Artifact | Score | What the check found | Type | Reach | Last commit |
|---|---|---|---|---|---|
| arboretolilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today | |
| aws-cdk-developmentlilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today | |
| bidslilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today | |
| adaptyvlilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today | |
| analyze-fastalilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today | |
| ancestry-risk-profilerlilinji/GeneTind-Life-Skills | No license | Skill | 8 stars | today |
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