Version Compatibility

Reference examples tested with: DADA2 1.30+, ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+, vegan 2.6+

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.

Microbiome Pipeline

"Run end-to-end 16S microbiome analysis from FASTQ" -> Orchestrate DADA2 denoising, taxonomy assignment, alpha/beta diversity (phyloseq), differential abundance (ALDEx2/ANCOM-BC2), and functional prediction (PICRUSt2).

Pipeline Overview