HiCParser
This is the development version of HiCParser; to use it, please install the devel version of Bioconductor.
Parser for HiC data in R
Bioconductor version: Development (3.21)
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.
Author: Zytnicki Matthias [aut], Maigné Élise [aut, cre]
Maintainer: Maigné Élise <elise.maigne at inrae.fr>
citation("HiCParser")):
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("HiCParser")
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("HiCParser")| Introduction to HiCParser | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, HiC, Software |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | LGPL |
| Depends | |
| Imports | data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, GenomeInfoDb |
| System Requirements | |
| URL | https://github.com/emaigne/HiCParser |
| Bug Reports | https://github.com/emaigne/HiCParser/issues |
See More
| Suggests | rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HiCParser_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | HiCParser_0.99.7.tgz |
| macOS Binary (arm64) | HiCParser_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiCParser |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCParser |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCParser/ |
| Package Short Url | https://bioconductor.org/packages/HiCParser/ |
| Package Downloads Report | Download Stats |