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Bioconductor / SummarizedExperiment

A container (S4 class) for matrix-like assays
https://bioconductor.org/packages/SummarizedExperiment
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Conversion to SingleCellExpriment object #49

Closed zhli12 closed 3 years ago

zhli12 commented 3 years ago

Is there a way to convert SummarizedExperiment object to SingleCellExperiment object? My final goal is to create a Seurat object from the SummarizedExperiment object, but the conversion functions available can only be applied to SingleCellExperiment objects

hpages commented 3 years ago

Hi,

The SingleCellExperiment class extends the SummarizedExperiment class and is implemented in its own package (the SingleCellExperiment package). There are dozens of packages in Bioconductor that implement SummarizedExperiment extensions and it's up to each of them to support coercion back and forth to SummarizedExperiment. In other words this is a question you need to ask to the SingleCellExperiment folks, either on the Bioconductor support site (don't forget to tag your question with SingleCellExperiment and SummarizedExperiment), or on GitHub.

Best, H.