Workflow chapter using Visium breast cancer dataset

[lmweber]

Hi @estellad, thank you for getting in touch regarding adapting your workflow materials from the BC2 conference for inclusion in the book.

As we discussed by email, I'm opening some GitHub issues so we can keep track of the additions.

In this issue, we would like to add a workflow chapter using the Visium breast cancer dataset. This would be a useful addition since currently we do not have a workflow chapter using a cancer dataset.

The book is now reformatted in Quarto format, and new chapters can be added as new .qmd files.

The main constraint is that we would like to include only Bioconductor or CRAN packages in the runnable examples, since this will help with long-term maintenance, and make it possible to submit the book to Bioconductor and use the Bioconductor build systems. We would also like to exclude Seurat due to its customized object formats and dependencies.

Specifically, this means we can't use GitHub tools (e.g. RCTD) within the examples. For these sections, I would suggest discussing these tools in the text instead, and we could consider adding examples with Bioconductor tools at a later time if we find some Bioconductor tools for these steps that perform well.

For the datasets, we could save them in an ExperimentHub package so they can be loaded within the examples, similar to STexampleData. (We could also add the objects to STexampleData if you prefer.)

Also tagging @stephaniehicks @raphg