R3CPET

The software tool R3CPET identifies the most likely protein complexes that facilitate chromatin interactions and the areas they influence, enhancing chromatin conformation research. It uses a non-parametric Bayesian method to analyze data from ChIA-PET, transcription factor binding sites, and protein interactions. It delivers biologically meaningful and accurate predictions validated by experimental and simulation data. This tool offers significant insights into the proteins cooperating in chromatin interactions, advancing our understanding of chromatin dynamics.

Topic

Gene expression;Protein interactions;Nucleic acid sites, features and motifs;Nucleic acid structure analysis;Molecular modelling;ChIP-seq

Detail

  • Operation: Statistical inference;Pathway or network prediction;Protein-protein interaction prediction;Pathway or network visualisation

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU General Public License >=2

  • Cost: Free

  • Version name: 1.34.1

  • Credit: The National Basic Research Program of China, the National High Technology Research and Development Program of China, the National Nature Science Foundation of China, Tsinghua National Laboratory for Information Science and Technology Cross-discipline Foundation.

  • Input: -

  • Output: -

  • Contact: Mohamed Nadhir Djekidel djek.nad@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process.
  • Djekidel MN, et al. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. 2015; 16:288. doi: 10.1186/s13059-015-0851-6
  • https://doi.org/10.1186/s13059-015-0851-6
  • PMID: 26694485
  • PMC: PMC4716632

Download and documentation

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