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Workflow chapter using Xenium dataset

Open lmweber opened this issue 9 months ago • 1 comments

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

lmweber avatar Oct 06 '23 20:10 lmweber