HiCExperiment
This is the released version of HiCExperiment; for the devel version, see HiCExperiment.
Bioconductor class for interacting with Hi-C files in R
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| LICENSE | Text |
Details
| biocViews | DNA3DStructure, DataImport, HiC, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2) |
| Imports | InteractionSet, strawr, Seqinfo, 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 | HiSpaR, 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | HiCExperiment_1.12.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HiCExperiment_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | HiCExperiment_1.12.0.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/ |
| Package Downloads Report | Download Stats |