mariner

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see mariner.

Mariner: Explore the Hi-Cs

Bioconductor version: 3.20

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 iD ORCID: 0000-0003-4051-3217

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FunctionalGenomics, HiC, Software, Visualization

Version 1.6.0

In Bioconductor since BioC 3.17 (R-4.3) (2 years)

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/

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_1.6.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) mariner_1.6.0.tgz

macOS Binary (arm64) mariner_1.6.0.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/

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