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Bioconductor / SummarizedExperiment

A container (S4 class) for matrix-like assays
https://bioconductor.org/packages/SummarizedExperiment
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import / export as loom #5

Closed mtmorgan closed 6 years ago

mtmorgan commented 6 years ago

@hpages I implemented an .export_loom() function on the loom-export branch to complement makeSummarizedExperimentFromLoom(), but I was wondering where it really belongs? In some ways it could go in HDF5Array, with functionality like saveHDF5SummarizedExperimet(). And ultimately it could well end up in a loom package (see also loomR and hdf5r). Suggestions?

There are some pretty severe limitations on functionality, e.g., not supporting GRangesList, any of the *List or other column classes, or even factor levels.

dvantwisk commented 6 years ago

The features that @mtmorgan discussed here will be implemented in LoomExperiment https://github.com/Bioconductor/LoomExperiment. Further discussion on functionality and features should occur there.