mariner
This is the development version of mariner; for the stable release version, see mariner.
Mariner: Explore the Hi-Cs
Bioconductor version: Development (3.21)
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:
Maintainer: Eric Davis <ericscottdavis at outlook.com>
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")| Introduction to mariner | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, HiC, Software, Visualization |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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
| Suggests | knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mariner_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | mariner_1.7.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |