TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning
Stable version: http://bioconductor.org/packages/release/bioc/html/trena.html
Developmental version: http://www.trena.org
Metalysis and cis-Metalysis: Meta-analysis using combinations of cis-regulatory sequence motifs
Reference: http://www.pnas.org/content/109/26/E1801/1
Stable version: http://veda.cs.uiuc.edu/cisMetalysis/