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mariner

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

Mariner: Explore the Hi-Cs


Bioconductor version: Development (3.19)

Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

Author: Eric Davis [aut, cre]

Maintainer: Eric Davis <ericscottdavis at outlook.com>

Citation (from within R, enter citation("mariner")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mariner")

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("mariner")
Introduction to mariner HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FunctionalGenomics, HiC, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid
System Requirements
URL http://ericscottdavis.com/mariner/
See More
Suggests knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData
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Package Archives

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

Source Package mariner_1.3.0.tar.gz
Windows Binary mariner_1.3.0.zip (64-bit only)
macOS Binary (x86_64) mariner_1.3.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/mariner
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mariner
Bioc Package Browser https://code.bioconductor.org/browse/mariner/
Package Short Url https://bioconductor.org/packages/mariner/
Package Downloads Report Download Stats