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Documentation Status DOI install with bioconda Platforms

STARE - Look into TF regulation on gene level leveraging an adapted Activity-By-Contact score

STARE is a framework that combines two tasks, which can also work independently:

  • score enhancer-gene interactions with the Activity-By-Contact (ABC) model
  • derive TF affinities for regions

Those two parts are combined to summarise TF affinities on gene level, which allows for a variety of downstream analyses. If this sounds interesting to you, here's a full documentation on Read the Docs.

STARE_Logo

References

STARE and its application are described in our publication:

Hecker, D., Behjati Ardakani, F., Karollus, A., Gagneur, J., & Schulz, M. H. (2023). The adapted Activity-By-Contact model for enhancer–gene assignment and its application to single-cell data. Bioinformatics, 39(2), btad062. https://doi.org/10.1093/bioinformatics/btad062

The results of our analyses are available via Zenodo.

The framework is a combination and adaptation which is based on: