Rega
This is the development version of Rega; for the stable release version, see Rega.
R Interface to European Genome-Phenome Archive
Bioconductor version: Development (3.24)
The European Genome-phenome Archive (EGA) provides long-term storage and controlled sharing of personally identifiable genetic data. The Rega package offers a streamlined and extensible R interface to the EGA API, facilitating the programmatic upload of metadata. GEO-like Excel submission template is provided as a default method of organizing submission metadata.
Author: Igor Cervenka [aut, cre]
, Athimed El Taher [aut]
, Robert Ivanek [aut]
Maintainer: Igor Cervenka <igor.cervenka at unibas.ch>
citation("Rega")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Rega")
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("Rega")| The Rega User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software, ThirdPartyClient |
| Version | 1.1.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6) |
| Imports | askpass, httr2, jsonlite, jsonvalidate, keyring, readxl, rlang, stringr, tibble, tidyr, validate, yaml |
| System Requirements | |
| URL | https://github.com/ivanek/Rega |
| Bug Reports | https://github.com/ivanek/Rega/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | Rega_1.1.1.tar.gz |
| Windows Binary (x86_64) | Rega_1.1.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Rega_1.1.1.tgz |
| macOS Binary (sonoma-arm64) | Rega_1.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rega |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rega |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rega/ |
| Package Short Url | https://bioconductor.org/packages/Rega/ |
| Package Downloads Report | Download Stats |