• pychromVAR pychromVAR is a python package for inferring TF variability from scATAC-seq by re-implementing the method proposed in chromVAR.

  • scMEGA scMEGA is a R package designed to infer gene regulatory network by using single cell multi-omics data.

  • scOpen scOpen is a method for single-cell open chromatin analysis via NMF modelling.

  • RGT RGT is a Python package for integrative analysis of regulatory genomics data.