BICORN: An R package for integrative inference of de novo cis-regulatory modules

Abstract

BICORN is an R package developed to integrate prior transcription factor binding information and gene expression data for cis-regulatory module (CRM) inference. BICORN searches for a list of candidate CRMs from binary bindings on potential target genes. Applying Gibbs sampling, BICORN samples CRMs for each gene using the fitting performance of transcription factor activities and regulation strengths of TFs in each CRM on gene expression. Consequently, sparse regulatory networks are inferred as functional CRMs regulating target genes. The BICORN package is implemented in R and is available at https://cran.r-project.org/web/packages/BICORN/index.html.