mariner
This is thereleased version of mariner; for the devel version, seemariner.
Mariner: Explore the Hi-Cs
Bioconductor version: Release (3.22)
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: 0000-0003-4051-3217, Sarah Parker [aut] ORCID: 0000-0002-2700-3979
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")BiocManager::install("mariner")For older versions of R, please refer to the appropriateBioconductor 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 | 1.10.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 years) |
| License | MIT + fileLICENSE |
| 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 | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | mariner_1.10.0.tar.gz |
| Windows Binary (x86_64) | mariner_1.10.0.zip |
| macOS Binary (x86_64) | mariner_1.10.0.tgz |
| macOS Binary (arm64) | mariner_1.10.0.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 |