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README.md
# Save `SingleCellExperiment`s to file |Environment|Status| |---|---| |[BioC-release](https://bioconductor.org/packages/release/bioc/html/alabaster.sce.html)|[![Release OK](https://bioconductor.org/shields/build/release/bioc/alabaster.sce.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/alabaster.sce/)| |[BioC-devel](https://bioconductor.org/packages/devel/bioc/html/alabaster.sce.html)|[![Devel OK](https://bioconductor.org/shields/build/devel/bioc/alabaster.sce.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/alabaster.sce/)| The **alabaster.sce** package implements methods for saving and loading `SingleCellExperiment` objects under the **alabaster** framework. It provides a language-agnostic method for serializing reduced dimensions and alternative experiments along with the usual bits and pieces from the `SummarizedExperiment` parent class. To get started, install the package and its dependencies from Bioconductor: ```r # install.packages("BiocManager") BiocManager::install("alabaster.sce") ``` In the example below, we save a `SingleCellExperiment` object to file: ```r library(SingleCellExperiment) example(SingleCellExperiment, echo=FALSE) # can't be bothered to copy it here. sce ## class: SingleCellExperiment ## dim: 200 100 ## metadata(0): ## assays(2): counts logcounts ## rownames: NULL ## rowData names(0): ## colnames: NULL ## colData names(0): ## reducedDimNames(2): PCA tSNE ## mainExpName: NULL ## altExpNames(0): library(alabaster.sce) tmp <- tempfile() saveObject(sce, tmp) roundtrip <- readObject(tmp) class(roundtrip) ## [1] "SingleCellExperiment" ## attr(,"package") ## [1] "SingleCellExperiment" ```