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bio-microbiome-differential-abundance

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Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.

When to use

• Identifying differentially abundant taxa between experimental conditions
• Differential abundance testing for microbiome data
• Using ALDEx2 for CLR-transformed Welch's t-test
• Using ANCOM-BC2 for bias-corrected log-linear models
• Using MaAsLin2 for multivariable association
• Accounting for the compositional nature of microbiome data

When not to use

• Standard tests like t-test or DESeq2 without compositional adjustment
• Identifying overall differences first
• Enrichment of differential taxa

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