GitHub - AbbVie-ComputationalGenomics/SCArray: Large-scale single-cell RNA-seq data manipulation with GDS files (original) (raw)
Large-scale single-cell RNA-seq data manipulation using GDS files
GNU General Public License, GPLv3
Features
Large-scale single-cell RNA-seq data manipulation and statistical analysis with scalable implementation of generalized mixed models and principal component analysis. The package integrates the sparse matrix in Genomic Data Structure (GDS) files and the Bioconductor infrastructure framework to provide out-of-memory data storage and manipulation using the R programming language.
Bioconductor:
v1.6.0 (http://bioconductor.org/packages/SCArray/)
Package News: NEWS
Package Maintainer
Installation
- Requires R (≥ v3.5.0), gdsfmt (≥ v1.35.4)
- Bioconductor repository
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("SCArray")
Examples
suppressPackageStartupMessages(library(SCArray))
the GDS file for SingleCellExperiment
fn <- system.file("extdata", "example.gds", package="SCArray") sce <- scExperiment(fn)
sce
class: SingleCellExperiment
dim: 1000 850
metadata(0):
assays(1): counts
rownames(1000): MRPL20 GNB1 ... RPS4Y1 CD24
rowData names(0):
colnames(850): 1772122_301_C02 1772122_180_E05 ... 1772122_180_B06 1772122_180_D09
colData names(3): Cell_ID Cell_type Timepoint
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
counts(sce)