Declarations

Availability of data and material

The source code for the sevenC package is available on GitHub: https://github.com/ibn-salem/sevenC. The source code for all analyses in this manuscript is available on GitHub: https://github.com/ibn-salem/sevenC_analysis. All the genomic data used for analyses are freely available to be downloaded from the GEO repository or ENCODE as described in the methods section.

Competing interests

The authors declare that they have no competing interests.

Authors‘ contributions

JI developed and implemented the method, conceived the study and performed all analyses. MA supervised the study. JI and MA wrote the manuscript.

Acknowledgments

The authors thank all members of the CBDM group for fruitful discussions, especially Katerina Taškova for ideas on modeling and cross-validation. We further thank Idan Gabdank (Stanford University) for support in understanding ENCODE data set and updating it, Takaya Saito (University of Bergen) for updating and improving the precrec R package, Peter Hansen (Charité, Berlin) for support in ChIP-seq and ChIP-nexus analysis using Q, Morgane Thomas-Chollier (Ecole normale supérieure) for discussions on genome-wide motif analysis, and Sebastiaan Meijsing (Max Planck Institute for Molecular Genetics) for initial discussions on ChIP-exo profiles at chromatin loop anchors.