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Lifecycle: experimental rworkflows

fourDNData

fourDNData (read 4DN-Data) is a data package giving programmatic access to Hi-C contact files uniformly processed by the 4DN consortium.

The fourDNData() function provides a gateway to 4DN-hosted Hi-C files, including contact matrices (in .hic or .mcool) and other Hi-C derived files such as annotated compartments, domains, insulation scores, or pairs files.

The fourDNHiCExperiment() function recovers all 4DN-hosted Hi-C files associated with a single experimentSet Accession number.

library(fourDNData)
head(fourDNData())
fourDNData('4DNESDP9ECMN', type = 'compartments')
fourDNHiCExperiment('4DNESDP9ECMN')

HiCExperiment ecosystem

fourDNData is integrated within the HiCExperiment ecosystem in Bioconductor. Read more about the HiCExperiment class and handling Hi-C data in R here.

  • HiCExperiment: Parsing Hi-C files in R
  • HiCool: End-to-end integrated workflow to process fastq files into .cool and .pairs files
  • HiContacts: Investigating Hi-C results in R
  • HiContactsData: Data companion package
  • fourDNData: Gateway package to 4DN-hosted Hi-C experiments