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 (3.21)
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] (ORCID:
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
citation("HiCExperiment")):
Installation
To install this package, start R (version "4.5") 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 | 1.7.0 |
| 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 |
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_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |