HiCExperiment

Bioconductor class for interacting with Hi-C files in R

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews	DNA3DStructure, DataImport, HiC, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats
Linking To
Suggests	HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL	https://github.com/js2264/HiCExperiment
Bug Reports	https://github.com/js2264/HiCExperiment/issues

Depends On Me	DNAZooData, HiContacts, HiCool
Imports Me	fourDNData
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiCExperiment_1.0.0.tar.gz
Windows Binary	HiCExperiment_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	HiCExperiment_1.0.0.tgz
macOS Binary (arm64)	HiCExperiment_1.0.0.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