Orchestrating chromosome conformation capture analysis with Bioconductor
Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
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.
Topics & Concepts
BioconductorWorkflowChromosome conformation captureVisualizationGenomeComputer scienceComputational biologyChromosomeChromatinProcess (computing)Data miningBioinformaticsBiologyGeneticsDatabaseGeneProgramming languageEnhancerGene expressionGenomics and Chromatin DynamicsGene expression and cancer classificationGenomics and Phylogenetic Studies