BestPracticesST
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Workflow chapter using Xenium dataset
Following on from discussion in #42 @estellad
In this issue we are adding a workflow chapter using the Xenium dataset adapted from @estellad's BC2 workflow materials. This will also be a great addition, since we currently do not have any examples with a Xenium dataset.
As discussed in #42 , we prefer to avoid using Seurat objects, so we could try using MoleculeExperiment instead to load the data. The MoleculeExperiment
package includes a data loading function readXenium()
. I haven't worked with MoleculeExperiment
much yet myself though so please let me know how this goes. If this works, we could also add the MoleculeExperiment
object to STexampleData (or a separate similar package) to streamline loading in the examples.
Also tagging @stephaniehicks @raphg