Version Compatibility

Reference examples tested with: MSnbase 2.28+, ggplot2 3.5+, limma 3.58+, scanpy 1.10+, xcms 4.0+

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.

Metabolomics Pipeline

"Process my LC-MS metabolomics data end-to-end" -> Orchestrate XCMS peak detection, RT alignment, grouping, normalization/QC, metabolite annotation, statistical analysis, and pathway mapping for untargeted metabolomics.

Pipeline Overview