mariner

Mariner: Explore the Hi-Cs

Bioconductor version: 3.23 · Package version: 1.12.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mariner")

Details

Maintainer	Eric Davis <ericscottdavis@outlook.com>
Author	Eric Davis [aut, cre] (ORCID: <https://orcid.org/0000-0003-4051-3217>), Sarah Parker [aut] (ORCID: <https://orcid.org/0000-0002-2700-3979>)
License	MIT + file LICENSE
URL	https://ericscottdavis.com/mariner/, https://github.com/EricSDavis/mariner
Downloads rank	228
Source branch	RELEASE_3_23
biocViews	FunctionalGenomics, HiC, Software, Visualization

Documentation

Introduction to mariner

Download

Source package

Dependencies

Depends: R (>= 4.2.0)

Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, dplyr, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid

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

Reverse dependencies

Suggests Me (1): nullranges