WGCNA: In-depth Technical reports

Peter Langfelder

Dept. of Human Genetics, UC Los Angeles

Peter (dot) Langfelder (at) gmail (dot) com,

This page provides technical reports that discuss various features and options offered by the WGCNA R package. Most of these have not been described in detail in published articles.

Available reports

• What do TOMDenom settings mean?
• What is a signed TOM?

Min- vs. mean-denominator TOM

This report explains why using the minimum in the definition of Topological Overlap Measure (TOM) in weighted networks produces, in certain special situations, undesirable results, and how the undesirable results are avoided by replacing the minimum by the average.

• Technical report: Min- vs. mean denom TOM

Signed TOM

This report explains what signed Topological Overlap Measure (TOM) is and why it may be useful in unsigned networks. It also emphasizes that in signed networks, signed TOM is (practically) equal to the standard, unsigned TOM.

• Technical report: Signed TOM

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