preciseTAD

preciseTAD is a software tool for predicting chromosome conformation capture (Hi-C) domain boundaries at base-pair resolution. preciseTAD leverages an optimized transfer learning framework trained on high-resolution genome annotation data and provides accurate delineation of boundaries supported by strong experimental evidence. Notably, it can predict boundaries in cells lacking Hi-C data, offering a tool for understanding how genomic regulators shape the 3D structure of the genome at a finer resolution.

Topic

Transcription factors and regulatory sites;ChIP-seq;Machine learning;Protein expression;Chromosome conformation capture

Detail

  • Operation: Fold recognition;Transcription factor binding site prediction;Genome annotation

  • Software interface: Command-line user interface

  • Language: R

  • License: The MIT License

  • Cost: Free

  • Version name: 1.12.0

  • Credit: The PhRMA Foundation Research Informatics Award, the George and Lavinia Blick Research Fund scholarship.

  • Input: -

  • Output: -

  • Contact: Mikhail Dozmorov mikhail.dozmorov@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution
  • Stilianoudakis SC, Marshall MA, Dozmorov MG. preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution. Bioinformatics. 2022 Jan 12;38(3):621-630. doi: 10.1093/bioinformatics/btab743. PMID: 34741515; PMCID: PMC8756196.
  • https://doi.org/10.1093/bioinformatics/btab743
  • PMID: 34741515
  • PMC: PMC8756196

Download and documentation

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