HiCExperiment

Bioconductor class for interacting with Hi-C files in R

Bioconductor version: Release (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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNA3DStructure, DataImport, HiC, Software
Version	1.4.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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

Suggests	HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me	HiContacts, HiCool, DNAZooData
Imports Me	fourDNData, OHCA
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_1.4.0.tar.gz
Windows Binary (x86_64)	HiCExperiment_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	HiCExperiment_1.4.0.tgz
macOS Binary (arm64)	HiCExperiment_1.4.0.tgz
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