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Bioconductor - mariner (development version)

mariner

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

Mariner: Explore the Hi-Cs

Bioconductor version: Development (3.22)

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

Maintainer: Eric Davis <ericscottdavis at outlook.com>

Citation (from within R, enter citation("mariner")): 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("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")
Details biocViews FunctionalGenomics, HiC, Software, Visualization Version 1.9.0 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/ See More Package Archives

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

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