Version Compatibility

Reference examples tested with: R stats (base), edgeR 4.0+, ggplot2 3.5+, limma 3.58+

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 Analysis

"Compare cell populations between my conditions" → Test for significant changes in cell type frequencies (differential abundance) or marker expression levels (differential state) between experimental groups.

• R: CATALYST::testDA_edgeR() or diffcyt::testDA_GLMM()

Differential Abundance (DA)

Goal: Test which cell population clusters differ in frequency between experimental conditions.