mariner

DOI: 10.18129/B9.bioc.mariner  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see mariner.

Mariner: Explore the Hi-Cs

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Introduction to mariner
PDF		Reference Manual
Text		NEWS

Details

biocViews	FunctionalGenomics, HiC, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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
LinkingTo
Suggests	knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData
SystemRequirements
Enhances
URL	http://ericscottdavis.com/mariner/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	mariner_1.0.0.tar.gz
Windows Binary	mariner_1.0.0.zip
macOS Binary (x86_64)	mariner_1.0.0.tgz
macOS Binary (arm64)	mariner_1.0.0.tgz
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