HiCExperiment
Bioconductor class for interacting with Hi-C files in R
Bioconductor version: 3.24 · Package version: 1.13.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCExperiment")Details
| Maintainer | Jacques Serizay <jacquesserizay@gmail.com> |
| Author | Jacques Serizay [aut, cre] (ORCID: <https://orcid.org/0000-0002-4295-0624>) |
| License | MIT + file LICENSE |
| URL | https://github.com/js2264/HiCExperiment |
| Bug Reports | https://github.com/js2264/HiCExperiment/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNA3DStructure, DataImport, HiC, Software |
| Package Short Url | https://bioconductor.org/packages/HiCExperiment/ |
Citation
From within R, enter citation("HiCExperiment"):
Jacques Serizay. HiCExperiment: Bioconductor class for interacting with Hi-C files in R. doi:10.18129/B9.bioc.HiCExperiment, R package version 1.13.0, https://bioconductor.org/packages/HiCExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiCExperiment_1.13.0.tar.gz |
| Windows binary (x86_64) | HiCExperiment_1.13.0.zip |
| macOS binary (arm64) | HiCExperiment_1.13.0.tgz |
| macOS binary (x86_64) | HiCExperiment_1.13.0.tgz |
Dependencies
Depends: R (>= 4.2)
Imports: InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats
Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Reverse dependencies
Depends On Me (3): DNAZooData, HiContacts, HiCool
Imports Me (2): fourDNData, HiSpaR