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coexpression-networks

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Build weighted gene co-expression networks to identify modules of co-regulated genes, relate them to phenotypes, and find hub genes using WGCNA, hdWGCNA, MEGENA, CEMiTool, and Gaussian graphical models. Covers signed-network choice, soft-threshold selection, module preservation, and the marginal-vs-partial-correlation distinction. Use when finding co-expression modules, identifying hub genes, relating gene networks to clinical or experimental traits, or building single-cell co-expression networks. For directed TF-target inference see scenic-regulons and grn-inference; for condition rewiring see differential-networks.

When to use

• finding co-expression modules
• identifying hub genes
• relating gene networks to clinical or experimental traits
• building single-cell co-expression networks
• module discovery and trait association
• distinguishing direct from indirect edges

When not to use

• directed TF-target inference
• condition rewiring
• differential networks

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