RegSeq package contains the proposed RegSeq algorithm (function Reg_Finding), which is designed to perform the regulon analysis for RNA-Seq data, especially in small sample scenario. RegSeq can identify the key regulons that are most responsible for the difference in two groups samples.
See the attached User Tutorial file for more details.
Duanchen Sun and Zheng Xia (2018): RegSeq: A novel GSEA-based algorithm to perform the regulon analysis on RNA-Seq data with small sample replicates (In preparation).