SCArray
This is the development version of SCArray; for the stable release version, see SCArray.
Large-scale single-cell omics data manipulation with GDS files
Bioconductor version: Development (3.21)
Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.
Author: Xiuwen Zheng [aut, cre] (ORCID:
Maintainer: Xiuwen Zheng <xiuwen.zheng at abbvie.com>
citation("SCArray")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SCArray")
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("SCArray")| Overview | HTML | |
| Single-cell RNA-seq data manipulation using GDS files | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, RNASeq, SingleCell, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), gdsfmt(>= 1.36.0), methods, DelayedArray(>= 0.31.5) |
| Imports | S4Vectors, utils, Matrix, SparseArray(>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular |
| System Requirements | |
| URL | https://github.com/AbbVie-ComputationalGenomics/SCArray |
See More
| Suggests | BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array |
| Linking To | |
| Enhances | |
| Depends On Me | SCArray.sat |
| 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 | SCArray_1.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SCArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SCArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/SCArray/ |
| Package Short Url | https://bioconductor.org/packages/SCArray/ |
| Package Downloads Report | Download Stats |