bio-ecological-genomics-landscape-genomics
Tests genotype-environment associations and identifies loci under local adaptation using LFMM2 (LEA), pcadapt outlier detection, OutFLANK Fst-based selection scans, and redundancy analysis. Detects adaptive genetic variation correlated with environmental variables while controlling for population structure. Use when identifying adaptive loci across environmental gradients, testing for signatures of local adaptation, or predicting genetic vulnerability to climate change with gradientForest.
npx skills add BioTender-max/awesome-bio-agent-skills --skill landscape-genomics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: vegan 2.6+ 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. # Landscape Genomics **"Find loci associated with environmental adaptation in my populations"** → Test genotype-environment associations using LFMM2 latent factor mixed models or pcadapt outlier detection while controlling for population structure, and predict climate vulnerability with gradientForest. - R: `LEA::lfmm2()` for genotype-environment association testing - R: `pcadapt::pcadapt()` for selection scan without environmental data Identifies loci under local adaptation by testing genotype-environment associations while controlling for population structure. ## Population Structure Estimation with LEA **Goal:** Determine the number of ancestral populations (K) as a prerequisite for genotype-environment association testing. **Approach:** Run sNMF on genotype data across K=1-10 and select the K with minim
- Version Compatibility
- Population Structure Estimation with LEA
- LFMM2 Genotype-Environment Association
- Multiple Environmental Variables
- pcadapt Outlier Detection
- OutFLANK Fst-Based Selection Scan
- RDA-Based GEA
- gradientForest: Allele Turnover Prediction
- Environmental Data Extraction with terra
- Related Skills
What does the bio-ecological-genomics-landscape-genomics skill do?
Tests genotype-environment associations and identifies loci under local adaptation using LFMM2 (LEA), pcadapt outlier detection, OutFLANK Fst-based selection scans, and redundancy analysis. Detects adaptive genetic variation correlated with environmental variables while controlling for population structure. Use when identifying adaptive loci across environmental gradients, testing for signatures of local adaptation, or predicting genetic vulnerability to climate change with gradientForest.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill landscape-genomics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.