Workflow chapter using Xenium dataset

[lmweber]

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

[estellad]

Hi Lukas, thank you for the organization! So far ME works (on the github dev version (1.1.3), not the Bioc version (1.0.2)), but very bulky to load transcript-level ME and then coerce to single-cell level resolution SPE. In addition, readXenium() does not retain genewise metadata (in .h5) for easy subsetting to non-negative control probes. Meanwhile, readCosmx() and readMerscope() does not have genewise metadata to read in, so ME to SPE coercion is fine, but still bulky. Please see my issue on ME here, and my pull request for SPE here.

Most ST research nowadays are at spot or cell level, so there is no need for transcript-level plotting etc. yet. Therefore, I think there is no rush to add ME to STexampleData or ExperimentHub yet, if we can directly load new technologies using SPE constructor.