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Table 1 Comparison of key differences between wTO, WGCNA and ARACNe

From: wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool

Method

wTO

WGCNA

ARACNe

Topological overlap

Yes

Yes

No

Signed topological overlap

Optional

No

No

Consensus topological overlap

Weighted sum

Minimum weight (strict)

No

Pairwise p-values

Yes

No

Used to filter MI

Network view

Native

Exported to Cytoscape

Exported to Cytoscape

Soft thresholding

No

Optional (on by default)

No

Correlation choices

Spearman, Pearson

Bicor, Pearson

Spearman, Pearson, Kendall

Able to deal with time-series

Yes

No

No