SparseArray
High-performance sparse data representation and manipulation in R
Bioconductor version: 3.24 · Package version: 1.13.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SparseArray")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| Author | Hervé Pagès [aut, cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>), Vince Carey [fnd] (ORCID: <https://orcid.org/0000-0003-4046-0063>), Rafael A. Irizarry [fnd] (ORCID: <https://orcid.org/0000-0002-3944-4309>), Jacques Serizay [ctb] (ORCID: <https://orcid.org/0000-0002-4295-0624>) |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/SparseArray |
| Bug Reports | https://github.com/Bioconductor/SparseArray/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/SparseArray/ |
Citation
From within R, enter citation("SparseArray"):
Hervé Pagès. SparseArray: High-performance sparse data representation and manipulation in R. doi:10.18129/B9.bioc.SparseArray, R package version 1.13.3, https://bioconductor.org/packages/SparseArray.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SparseArray_1.13.3.tar.gz |
| Windows binary (x86_64) | SparseArray_1.13.3.zip |
| macOS binary (arm64) | SparseArray_1.13.3.tgz |
| macOS binary (x86_64) | SparseArray_1.13.3.tgz |
Dependencies
Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.13.1)
Imports: utils, stats, matrixStats, IRanges, XVector
LinkingTo: S4Vectors, IRanges, XVector
Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle
Reverse dependencies
Depends On Me (7): DelayedArray, DelayedRandomArray, DuckDBArray, h5mread, HDF5Array, TileDBArray, ZarrArray
Imports Me (22): alabaster.matrix, BatChef, batchelor, beachmat, BiocDuckDB, DelayedMatrixStats, DelayedTensor, dreamlet, DropletUtils, DuckDBDataFrame, glmGamPoi, GSVA, IDLFM, SCArray, scater, scone, scrapper, scRNAseq, scuttle, spatialdataR, TSCAN, zellkonverter
Suggests Me (5): BiocGenerics, MatrixGenerics, metagenomeSeq, S4Arrays, SummarizedExperiment