Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-microbiome-diversity-analysis

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-microbiome-diversity-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics — metagenomics & microbiomealpha

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-diversity-analysis

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

R: phyloseq::estimate_richness() for alpha, phyloseq::ordinate() for beta.
R: vegan::adonis2() for PERMANOVA testing.
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.
alpha_div <- estimate_richness(ps, measures = c('Observed', 'Chao1', 'Shannon', 'Simpson')) alpha_div$SampleID <- rownames(alpha_div) alpha_div <- merge(alpha_div, sample_data(ps), by = 'row.names').

Source Doc

Excerpt From SKILL.md

Statistical test

kruskal.test(Shannon ~ Group, data = alpha_div)

Pairwise comparisons

pairwise.wilcox.test(alpha_div$Shannon, alpha_div$Group, p.adjust.method = 'BH')


## Alpha Diversity Plots

```r
plot_richness(ps, x = 'Group', measures = c('Observed', 'Shannon')) +
    geom_boxplot() +
    theme_minimal()

Use cases

Use when comparing community composition across samples or testing for group differences in microbiome structure.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

amplicon-processing - Generate ASV table
differential-abundance - Identify taxa driving differences
data-visualization/ggplot2-fundamentals - Custom diversity plots
ecological-genomics/biodiversity-metrics - Hill number coverage-based rarefaction for ecological data
ecological-genomics/community-ecology - Constrained ordination and indicator species