HiCExperiment

DOI: 10.18129/B9.bioc.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 (3.18)

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")

# 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")

 

HTML R Script Introduction to HiCExperiment
PDF   Reference Manual
Text   LICENSE

Details

biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.1.2
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
LinkingTo
Suggests HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/js2264/HiCExperiment
BugReports 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_1.1.2.tar.gz
Windows Binary HiCExperiment_1.1.2.zip
macOS Binary (x86_64) HiCExperiment_1.1.2.tgz
macOS Binary (arm64) HiCExperiment_1.1.2.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

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