HiCExperiment

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HiCExperiment.

Bioconductor class for interacting with Hi-C files in R

Bioconductor version: 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/

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