HiCExperiment

This is the development version of HiCExperiment; for the stable release version, see HiCExperiment.

Bioconductor class for interacting with Hi-C files in R

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DOI: 10.18129/B9.bioc.HiCExperiment

Bioconductor version: Development (3.23)

R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.

Author: Jacques Serizay [aut, cre] ORCID iD ORCID: 0000-0002-4295-0624

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Citation (from within R, enter citation("HiCExperiment")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("HiCExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.