S4Arrays
This is the released version of S4Arrays; for the devel version, see S4Arrays.
Foundation of array-like containers in Bioconductor
Bioconductor version: Release (3.23)
The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).
Author: Hervé Pagès [aut, cre]
, Jacques Serizay [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("S4Arrays")):
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("S4Arrays")
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("S4Arrays")| A quick overview of the S4Arrays package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), methods, Matrix, abind, BiocGenerics(>= 0.45.2), S4Vectors(>= 0.47.6), IRanges |
| Imports | stats |
| System Requirements | |
| URL | https://bioconductor.org/packages/S4Arrays |
| Bug Reports | https://github.com/Bioconductor/S4Arrays/issues |
See More
| Suggests | BiocParallel, SparseArray(>= 0.0.4), DelayedArray, HDF5Array, testthat, knitr, rmarkdown, BiocStyle |
| Linking To | S4Vectors |
| Enhances | |
| Depends On Me | DelayedArray, SparseArray |
| Imports Me | alabaster.matrix, DelayedTensor, dreamlet, FLAMES, GSVA, h5mread, HDF5Array, ImageArray, scran, scuttle, SummarizedExperiment, ZarrArray |
| Suggests Me | BiocGenerics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | S4Arrays_1.12.0.tar.gz |
| Windows Binary (x86_64) | S4Arrays_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | S4Arrays_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | S4Arrays_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/S4Arrays |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/S4Arrays |
| Bioc Package Browser | https://code.bioconductor.org/browse/S4Arrays/ |
| Package Short Url | https://bioconductor.org/packages/S4Arrays/ |
| Package Downloads Report | Download Stats |