Rarr
This is the released version of Rarr; for the devel version, see Rarr.
Read Zarr Files in R
Bioconductor version: Release (3.23)
The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.
Author: Mike Smith [aut, ccp] (ORCID:
, Maintainer from 2022 to 2025.), Hugo Gruson [aut, cre]
, Artür Manukyan [ctb], Sharla Gelfand [ctb], German Network for Bioinformatics Infrastructure - de.NBI [fnd]
Maintainer: Hugo Gruson <hugo.gruson at embl.de>
citation("Rarr")):
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("Rarr")
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("Rarr")| Design principles for the Rarr package | HTML | |
| Supported Zarr features in Rarr | HTML | R Script |
| Working with Zarr arrays in R | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, Software |
| Version | 2.0.1 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | curl, jsonlite, lifecycle, paws.storage, R.utils, utils |
| System Requirements | GNU make |
| URL | https://huber-group-embl.github.io/Rarr/ https://github.com/Huber-group-EMBL/Rarr |
| Bug Reports | https://github.com/Huber-group-EMBL/Rarr/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), withr, ZarrArray |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ImageArray, ZarrArray |
| Suggests Me | anndataR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Rarr_2.0.1.tar.gz |
| Windows Binary (x86_64) | Rarr_2.0.1.zip |
| macOS Binary (big-sur-x86_64) | Rarr_2.0.1.tgz |
| macOS Binary (sonoma-arm64) | Rarr_2.0.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rarr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rarr |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rarr/ |
| Package Short Url | https://bioconductor.org/packages/Rarr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |