New features

Added new metrics:
- transcription factor cluster specificity
- median coexpression score of transcription factors and their target genes
Updated centrality metrics:
- for regulons where closeness and betweenness are not defined at the cluster level (e.g., when the TF doesn’t have incoming edges), the closeness and betweenness values are now computed based on the original network after motif mapping filtering
- per-cluster closeness and betweenness are always assigned better ranks compared to the original closeness and betweenness values
Improved TF prioritization in the Reference procedure (used when a list of (GO) terms of interest is specified by the user)
New parameter: users can now specify a custom background for the enrichment analysis (when not specified, the background defaults to the list of genes that are present in the expression matrix)
Expanded input options: terms of interest can now also be specified as ontology terms (e.g., GO:0009819), in addition to (or instead of) plain English words (e.g., drought)

Improvements and bug fixes

Full Changelog: v2.2...v3.0