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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


Bioconductor version: Development (3.19)

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]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HiCExperiment")
Introduction to HiCExperiment HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats
System Requirements
URL https://github.com/js2264/HiCExperiment
Bug Reports https://github.com/js2264/HiCExperiment/issues
See More
Suggests HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me DNAZooData, HiContacts, HiCool
Imports Me fourDNData
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiCExperiment_1.3.0.tar.gz
Windows Binary HiCExperiment_1.3.0.zip (64-bit only)
macOS Binary (x86_64) HiCExperiment_1.3.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiCExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCExperiment
Bioc Package Browser https://code.bioconductor.org/browse/HiCExperiment/
Package Short Url https://bioconductor.org/packages/HiCExperiment/
Package Downloads Report Download Stats