Version Compatibility

Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+

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.

Differential Abundance Testing

"Find which taxa differ between my groups" → Identify differentially abundant taxa between experimental conditions using compositionally-aware methods that account for the relative nature of microbiome data.

• R: ALDEx2::aldex() for CLR-transformed Welch's t-test
• R: ANCOMBC::ancombc2() for bias-corrected log-linear models
• R: Maaslin2::Maaslin2() for multivariable association

The Compositionality Problem