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Bioconductor - HiCParser (development version)

HiCParser

This is the development version of HiCParser; for the stable release version, see HiCParser.

Parser for HiC data in R

Bioconductor version: Development (3.22)

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 (from within R, enter 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")
Details biocViews DataImport, HiC, Software Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) 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 Package Archives

Follow Installation instructions to use this package in your R session.

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