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.

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Repository: majiayu000/claude-skill-registry
Last source activity: June 23, 2026 at 12:15
Detected SKILL.md language: English
Stars: 543
Forks: 85

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# Calculate multiple metrics
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')

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

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

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

# Custom plot
ggplot(alpha_div, aes(x = Group, y = Shannon, fill = Group)) +
    geom_boxplot() +
    geom_jitter(width = 0.2, alpha = 0.5) +
    theme_minimal() +
    labs(y = 'Shannon Diversity Index')

library(picante)

# Requires phylogenetic tree in phyloseq object
# Build tree from ASV sequences
library(DECIPHER)
library(phangorn)

seqs <- refseq(ps)
alignment <- AlignSeqs(seqs, anchor = NA)
phang_align <- phyDat(as(alignment, 'matrix'), type = 'DNA')
dm <- dist.ml(phang_align)
tree <- NJ(dm)
tree <- midpoint(tree)
phy_tree(ps) <- tree

# Calculate Faith's PD
otu_mat <- as.matrix(t(otu_table(ps)))
faith_pd <- pd(otu_mat, phy_tree(ps), include.root = TRUE)
alpha_div$PD <- faith_pd$PD

# Check if sequencing depth is adequate
rarecurve_data <- vegan::rarecurve(t(otu_table(ps)), step = 100, sample = min(sample_sums(ps)))

# ggplot version with ggrare (install from GitHub)
# devtools::install_github('gauravsk/ranacapa')
library(ranacapa)
p_rare <- ggrare(ps, step = 100, color = 'Group', se = FALSE)
p_rare + theme_minimal() + labs(title = 'Rarefaction Curves')

# Check sequencing depth
sample_sums(ps)

# Rarefy to minimum depth
ps_rarefied <- rarefy_even_depth(ps, sample.size = min(sample_sums(ps)),
                                  rngseed = 42, replace = FALSE)

# Calculate distance matrices
bray <- phyloseq::distance(ps, method = 'bray')       # Bray-Curtis
jaccard <- phyloseq::distance(ps, method = 'jaccard') # Jaccard
unifrac <- UniFrac(ps, weighted = TRUE)               # Weighted UniFrac (requires tree)

# Ordination
ord_bray <- ordinate(ps, method = 'PCoA', distance = bray)

# Plot
plot_ordination(ps, ord_bray, color = 'Group') +
    stat_ellipse(level = 0.95) +
    theme_minimal()

# Test for group differences
metadata <- data.frame(sample_data(ps))
permanova_result <- adonis2(bray ~ Group, data = metadata, permutations = 999)
permanova_result

# With covariates
adonis2(bray ~ Group + Age + Sex, data = metadata, permutations = 999)

# Test homogeneity of dispersions (assumption of PERMANOVA)
beta_disp <- betadisper(bray, metadata$Group)
permutest(beta_disp)
plot(beta_disp)

ord_nmds <- ordinate(ps, method = 'NMDS', distance = bray)

# Check stress
ord_nmds$stress  # Should be < 0.2

plot_ordination(ps, ord_nmds, color = 'Group') +
    theme_minimal()

Metric	Type	Considers Abundance	Phylogeny
Bray-Curtis	Quantitative	Yes	No
Jaccard	Binary	No	No
UniFrac (unweighted)	Binary	No	Yes
UniFrac (weighted)	Quantitative	Yes	Yes

bio-microbiome-diversity-analysis

Install options

Review the source files

Diversity Analysis

Create phyloseq Object

Diversity Analysis

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

name	bio-microbiome-diversity-analysis
description	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.
tool_type	r
primary_tool	phyloseq

bio-microbiome-diversity-analysis

Source facts

Install options

Review the source files

More from this repository

More from this repository

Diversity Analysis

Create phyloseq Object

Diversity Analysis

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