Version Compatibility

Reference examples tested with: WGCNA 1.72+, hdWGCNA 0.3+, CEMiTool 1.26+, GENIE3-adjacent GGM via GeneNet 1.2.16+.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

WGCNA argument defaults differ by entry point: pickSoftThreshold() and blockwiseModules() default to networkType='unsigned'. The signed-network choice (below) must be set identically at every step or the soft power and modules silently mismatch.

Co-expression Networks

"Find co-expression modules and hub genes from my expression data" -> Build a weighted gene co-expression network, detect modules of co-regulated genes by clustering a topological-overlap dissimilarity, summarize each module by its eigengene, and relate modules to sample traits.

• R: WGCNA::blockwiseModules() for network construction + module detection (bulk)
• R: hdWGCNA metacell workflow for single-cell expression
• R: GeneNet/graphical lasso when direct (not indirect) edges are required