JRIM is a package for Jointly Reconstructing cis-regulatory Interaction Maps of multiple cell populations using single-cell chromatin accessibility data and identifying shared and common interaction patterns. It uses an aggregation process to deal with the sparsity of single-cell data, exploits similarity between cell types via a group lasso penalty, and generates comparable networks. JRIM could be used to characterize difference between cell types or identify dynamic changes during cell development.
cis-Browser (cis-Regulatory Browser) is genome browser for cis-regulatory information inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation