bio-microbiome-diversity-analysis
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-diversity-analysis --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: R stats (base), ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+, 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. # Diversity Analysis **"Compare microbial diversity across my samples"** → Calculate alpha diversity (within-sample richness/evenness) and beta diversity (between-sample dissimilarity) to test for community composition differences across groups. - R: `phyloseq::estimate_richness()` for alpha, `phyloseq::ordinate()` for beta - R: `vegan::adonis2()` for PERMANOVA testing ## Create phyloseq Object ```r library(phyloseq) library(vegan) library(ggplot2) seqtab <- readRDS('seqtab_nochim.rds') taxa <- readRDS('taxa.rds') metadata <- read.csv('sample_metadata.csv', row.names = 1) ps <- phyloseq(otu_table(seqtab, taxa_are_rows = FALSE), tax_table(taxa), sample_data(metadata)) taxa_names(ps) <- paste0('ASV', seq(ntaxa(ps))) ``` ## Alpha Diversity ```r # Calc
- Version Compatibility
- Create phyloseq Object
- Alpha Diversity
- Alpha Diversity Plots
- Faith's Phylogenetic Diversity
- Rarefaction Curves
- Rarefaction
- Beta Diversity
- PERMANOVA
- Beta Dispersion
- NMDS Ordination
- Distance Metrics Comparison
- Related Skills
What does the bio-microbiome-diversity-analysis skill do?
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-diversity-analysis --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.