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数据与复现
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bio-microbiome-diversity-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-diversity-analysis
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- R：phyloseq：：estimate_richness() ，用于 alpha，phyloseq：：ordinate() ，用于 beta。
- R：vegan：：adonis2() ，用于 PERMANOVA testing。
- 比较 microbial diversity across my samples" → Calculate alpha diversity (within-sample richness/evenness) 、 beta diversity (between-sample dissimilarity) to test ，用于 community composition differences across groups. R：phyloseq：：estimate_richness() ，用于 alpha，phyloseq：：ordinate() ，用于 beta R：vegan：：adonis2() ，用于 PERMANOVA testing。
- alpha_div <- estimate_richness(ps，measures = c('Observed'，'Chao1'，'Shannon'，'Simpson')) alpha_div$SampleID <- rownames(alpha_div) alpha_div <- merge(alpha_div，sample_data(ps)，by = 'row.names')。
原始文档
SKILL.md 摘录
Statistical test
kruskal.test(Shannon ~ Group, data = alpha_div)
Pairwise comparisons
pairwise.wilcox.test(alpha_div$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()
适用场景
- 适合在comparing community composition across samples 或 testing ，用于 group differences in microbiome structure时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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
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