savingBiocObjects
This is the development version of savingBiocObjects; to use it, please install the devel version of Bioconductor.
Saving Bioconductor Objects for Sharing
Bioconductor version: Development (3.24)
Documentation and guidance on strategies for saving and sharing Bioconductor objects, covering RDS serialization, HDF5-backed storage, the alabaster ecosystem for cross-language interoperability, exporting genomic ranges to standard formats, and preserving object metadata.
Author: Michael Love [aut, cre]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("savingBiocObjects")):
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("savingBiocObjects")
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("savingBiocObjects")| savingBiocObjects.html | HTML | R Script |
Details
| biocViews | BasicWorkflow, Workflow |
| Version | 0.99.0 |
| License | MIT + file LICENSE |
| Depends | |
| Imports | |
| System Requirements | Quarto (https://quarto.org) |
| URL | https://mikelove.github.io/savingBiocObjects |
| Bug Reports | https://github.com/mikelove/savingBiocObjects/issues |
See More
| Suggests | SummarizedExperiment, SingleCellExperiment, GenomicRanges, HDF5Array, anndataR, alabaster.base, alabaster.se, rtracklayer, plyranges, jsonlite, BiocManager, knitr, quarto |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | savingBiocObjects_0.99.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/savingBiocObjects |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/savingBiocObjects |
| Package Short Url | https://bioconductor.org/packages/savingBiocObjects/ |
| Package Downloads Report | Download Stats |