HiCParser
Parser for HiC data in R
Bioconductor version: 3.24 · Package version: 1.5.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCParser")Details
| Maintainer | Maigné Élise <elise.maigne@inrae.fr> |
| Author | Zytnicki Matthias [aut], Maigné Élise [aut, cre] |
| License | LGPL |
| URL | https://github.com/emaigne/HiCParser |
| Bug Reports | https://github.com/emaigne/HiCParser/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, HiC, Software |
| Package Short Url | https://bioconductor.org/packages/HiCParser/ |
Citation
From within R, enter citation("HiCParser"):
Zytnicki Matthias, Maigné Élise. HiCParser: Parser for HiC data in R. doi:10.18129/B9.bioc.HiCParser, R package version 1.5.1, https://bioconductor.org/packages/HiCParser.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiCParser_1.5.1.tar.gz |
| Windows binary (x86_64) | HiCParser_1.5.1.zip |
| macOS binary (arm64) | HiCParser_1.5.1.tgz |
| macOS binary (x86_64) | HiCParser_1.5.1.tgz |
Dependencies
Imports: data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, Seqinfo
LinkingTo: Rcpp
Suggests: rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)