footprint-tools: digital genomic footprint detection and analysis#

A Python package for de novo detection of genomic footprints from DNase I data.


  • De novo footprint detection

  • Consensus footprint detection (emperical Bayes)

  • Differential footprinting

  • API for programmatic access to cleavage data directly from sequence alignment files


Please note that is documentation is a work in progress. Please contact us with any questions.


Pre-processed data#

As part of the ENCODE Consortium we have generated digital genomic footprinting data for >240 cell types and tissues. These data and their metadata are hosted at both and ZENDODO.



Vierstra, J., Lazar, J., Sandstrom, R. et al. Global reference mapping of human transcription factor footprints. Nature 583, 729–736 (2020)