mariner
This is the development version of mariner; for the stable release version, see mariner.
Mariner: Explore the Hi-Cs
Bioconductor version: Development (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.
Maintainer: Eric Davis <ericscottdavis at outlook.com>
citation("mariner")
):
Installation
To install this package, start R (version "4.4") 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 | 1.5.0 |
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_1.5.0.tar.gz |
Windows Binary | mariner_1.5.0.zip |
macOS Binary (x86_64) | mariner_1.5.0.tgz |
macOS Binary (arm64) | mariner_1.5.0.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/ |
Package Downloads Report | Download Stats |