SparseArray
This is the development version of SparseArray; for the stable release version, see SparseArray.
High-performance sparse data representation and manipulation in R
Bioconductor version: Development (3.24)
The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.
Author: Hervé Pagès [aut, cre]
, Vince Carey [fnd]
, Rafael A. Irizarry [fnd]
, Jacques Serizay [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("SparseArray")):
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("SparseArray")
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("SparseArray")| SparseArray objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.13.2 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0), methods, Matrix, BiocGenerics(>= 0.43.1), MatrixGenerics(>= 1.11.1), S4Vectors(>= 0.43.2), S4Arrays(>= 1.11.1) |
| Imports | utils, stats, matrixStats, IRanges, XVector |
| System Requirements | |
| URL | https://bioconductor.org/packages/SparseArray |
| Bug Reports | https://github.com/Bioconductor/SparseArray/issues |
See More
| Suggests | HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle |
| Linking To | S4Vectors, IRanges, XVector |
| Enhances | |
| Depends On Me | DelayedArray, DelayedRandomArray, h5mread, HDF5Array, TileDBArray, ZarrArray |
| Imports Me | alabaster.matrix, BatChef, batchelor, beachmat, DelayedMatrixStats, DelayedTensor, dreamlet, DropletUtils, glmGamPoi, GSVA, SCArray, scater, scone, scrapper, scuttle, TSCAN, zellkonverter, scRNAseq, IDLFM |
| Suggests Me | BiocGenerics, MatrixGenerics, metagenomeSeq, S4Arrays, SummarizedExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SparseArray_1.13.2.tar.gz |
| Windows Binary (x86_64) | SparseArray_1.13.2.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | SparseArray_1.13.2.tgz |
| macOS Binary (sonoma-arm64) | SparseArray_1.13.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SparseArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SparseArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/SparseArray/ |
| Package Short Url | https://bioconductor.org/packages/SparseArray/ |
| Package Downloads Report | Download Stats |