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Updated the README.
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LTLA committed Mar 16, 2024
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# Save `SummarizedExperiment`s to file

|Environment|Status|
|---|---|
|[BioC-release](https://bioconductor.org/packages/release/bioc/html/alabaster.se.html)|[![Release OK](https://bioconductor.org/shields/build/release/bioc/alabaster.se.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/alabaster.se/)|
|[BioC-devel](https://bioconductor.org/packages/devel/bioc/html/alabaster.se.html)|[![Devel OK](https://bioconductor.org/shields/build/devel/bioc/alabaster.se.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/alabaster.se/)|

The **alabaster.se** package implements methods for saving and loading `SummarizedExperiment` objects under the **alabaster** framework.
It provides a language-agnostic method for serializing experimental data and annotations in these objects, including the genomic coordinates in a `RangedSummarizedExperiment`.
To get started, install the package and its dependencies from GitHub:
To get started, install the package and its dependencies from Bioconductor:

```r
devtools::install_github("ArtifactDB/alabaster.schemas")
devtools::install_github("ArtifactDB/alabaster.base")
devtools::install_github("ArtifactDB/alabaster.ranges")
devtools::install_github("ArtifactDB/alabaster.matrix")
devtools::install_github("ArtifactDB/alabaster.se")
# install.packages("BiocManager")
BiocManager::install("alabaster.matrix")
```

In the example below, we save a `RangedSummarizedExperiment` object to file:
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library(alabaster.se)
tmp <- tempfile()
dir.create(tmp)
meta <- stageObject(se, tmp, "se")
meta[["$schema"]]
## [1] "summarized_experiment/v1.json"
saveObject(rse, tmp)

roundtrip <- loadObject(meta, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "RangedSummarizedExperiment"
## attr(,"package")
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