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Orchestrating chromosome conformation capture analysis with Bioconductor

Author

Listed:
  • Jacques Serizay

    (Université Paris Cité, Unité Régulation Spatiale des Génomes)

  • Cyril Matthey-Doret

    (Université Paris Cité, Unité Régulation Spatiale des Génomes
    Sorbonne Université, Collège Doctoral
    École Polytechnique Fédérale de Lausanne)

  • Amaury Bignaud

    (Université Paris Cité, Unité Régulation Spatiale des Génomes
    Sorbonne Université, Collège Doctoral)

  • Lyam Baudry

    (Université Paris Cité, Unité Régulation Spatiale des Génomes
    Sorbonne Université, Collège Doctoral
    Université de Lausanne, Center for Integrative Genomics, Quartier Sorge)

  • Romain Koszul

    (Université Paris Cité, Unité Régulation Spatiale des Génomes)

Abstract

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.

Suggested Citation

  • Jacques Serizay & Cyril Matthey-Doret & Amaury Bignaud & Lyam Baudry & Romain Koszul, 2024. "Orchestrating chromosome conformation capture analysis with Bioconductor," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44761-x
    DOI: 10.1038/s41467-024-44761-x
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