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differential-networks

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Compare gene co-expression and regulatory networks between biological conditions to find rewired relationships using DiffCorr, DiffCoEx, DINGO/iDINGO, and CoDiNA. Covers the differential-connectivity-is-not-differential-expression distinction, the pairwise multiple-testing explosion, marginal vs partial (direct) rewiring, and the underpowered-rewiring failure mode. Use when comparing co-expression networks between disease vs control, treatment, or developmental stages, or finding hub genes that rewire without changing mean expression. For single-condition modules see coexpression-networks; for differential expression of means see differential-expression/de-results.

When to use

• comparing co-expression networks between disease vs control
• comparing networks between treatment or developmental stages
• finding hub genes that rewire without changing mean expression
• identifying gained, lost, and reversed edges
• testing differential connectivity
• module-level rewiring analysis
• direct rewiring analysis using partial correlations
• multi-omics rewiring analysis

When not to use

• single-condition modules
• differential expression of means

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