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mariner (development version)

mariner

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

Mariner: Explore the Hi-Cs

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DOI: 10.18129/B9.bioc.mariner

Bioconductor version: Development (3.23)

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 , Sarah Parker [aut] ORCID iD ORCID: 0000-0002-2700-3979

Maintainer: Eric Davis <ericscottdavis at outlook.com>

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

Installation

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

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FunctionalGenomics, HiC, Software, Visualization

Version 1.11.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 years)

License MIT + file LICENSE

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 https://ericscottdavis.com/mariner/ https://github.com/EricSDavis/mariner

See More

Suggests knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData, TxDb.Hsapiens.UCSC.hg38.knownGene, fields

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me nullranges

Links To Me

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Package Archives

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

Source Package mariner_1.11.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

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/

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