mariner
This is the released version of mariner; for the devel version, see mariner.
Mariner: Explore the Hi-Cs
Bioconductor version: Release (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]
, Sarah Parker [aut]
Maintainer: Eric Davis <ericscottdavis at outlook.com>
citation("mariner")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | |
| LICENSE | Text |
Details
| biocViews | FunctionalGenomics, HiC, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| 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 |
| System Requirements | |
| URL | https://ericscottdavis.com/mariner/ https://github.com/EricSDavis/mariner |
See More
| Suggests | knitr, testthat (>= 3.0.0), rmarkdown, ExperimentHub, marinerData, TxDb.Hsapiens.UCSC.hg38.knownGene, fields |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | nullranges |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mariner_1.12.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | mariner_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | mariner_1.12.0.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 |