mariner

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Mariner: Explore the Hi-Cs

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-4051-3217 , Sarah Parker [aut] ORCID: 0000-0002-2700-3979

Maintainer: Eric Davis <ericscottdavis at outlook.com>

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

Eric Davis, Sarah Parker. mariner: Mariner: Explore the Hi-Cs. doi:10.18129/B9.bioc.mariner, R package version 1.13.1, https://bioconductor.org/packages/mariner.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FunctionalGenomics, HiC, Software, Visualization
Version	1.13.1
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, dplyr, 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	https://ericscottdavis.com/mariner/ https://github.com/EricSDavis/mariner

Suggests	knitr, testthat (>= 3.0.0), rmarkdown, ExperimentHub, marinerData, TxDb.Hsapiens.UCSC.hg38.knownGene, fields
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	nullranges
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	mariner_1.13.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	mariner_1.13.1.tgz
macOS Binary (sonoma-arm64)	mariner_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mariner
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mariner
Package Short Url	https://bioconductor.org/packages/mariner/
Package Downloads Report	Download Stats