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 (3.20)
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("HiCExperiment")
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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 | ||
LICENSE | Text |
Details
biocViews | DNA3DStructure, DataImport, HiC, Software |
Version | 1.5.2 |
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 |
See More
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_1.5.2.tar.gz |
Windows Binary | HiCExperiment_1.5.2.zip (64-bit only) |
macOS Binary (x86_64) | HiCExperiment_1.5.2.tgz |
macOS Binary (arm64) | HiCExperiment_1.5.2.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 |