Lesson todos

[nsohail19]

All lessons

• Add time estimate
• Zenodo citation missing

Lesson 01 - Spatial Transcriptomics Technologies

• (optional) Maybe a few exercises of scenarios where people would pick a technology to use for the research question

Lesson 05 - QC

• Maybe move the Spatial overlay to the second tab since we don't really discuss it and the discussion above is about the plot we don't see by default? NS note: I like having the visual upfront but I understand why the suggestion is to put it second. I am going to leave it as is and we can revisit based on feedback from the class

Lesson 10 - Seurat Cheatsheet

• "The following requested variables were not found: Spatial.008um_PTPRC" when using FetchData NS note: did not get this error
• On DimPlot do we like just the first few clusters being annotated?

Lesson 11 - Spatially Derived Clusters

• "plan("multicore", workers = parallel::detectCores() - 1)" returns "Warning message: In supportsMulticoreAndRStudio(...) : [ONE-TIME WARNING] Forked processing ('multicore') is not supported when running R from RStudio because it is considered unstable. For more details, how to control forked processing or not, and how to silence this warning in future R sessions, see ?parallelly::supportsMulticore"
• A bit more explanation of the split.scale argument
• Can you elaborate on this comment "# Sometimes when you merge dataframes, you lose rownames". Do you mean if you haven't specified the add.cell.id when merging?
• Link to O2/HPC materials
• "There appears to be 2 unique populations of B cells in our PCA space, where the orig.ident is driving the differences in those bins." I wonder if unique is the right way to describe this, it's the same B cell population just in different samples right?
• We have used latent space with reference to Harmony output a few times, so we should introduce the idea.
• "For one, we can see that there is less "noise" in the seurat_banksy clusters, where bins of a cluster are not as scattered throughout the slide." I don't know if I agree with this. They feel pretty similar to me. Maybe I need to see them even closer up.
• Unhappy with wording of text at end of lesson. WJG: I thought the wording was fine.
• Answer key needs updating for annotating cluster to celltypes
• Re-render lesson, could't do it on WJG computer

Lesson 12 - Deconvolution

• Aside lesson for generating reference has this sentence that ends abruptly at the end: "This is so that when we run subset() and specify downsample = 500, we will be" Otherwise, the aside looks good
• "First cell type predicted on the bead" and "Second cell type predicted on the bead for doublet" should bead be pixel/bin/spot/something else?
• "So we are going to do some data wrangling to ensure that we keep track of all information. Including those ~200 bins without first_type labels." Where/how do we keep track of these 200 rejected bins? I've tried adding "We will handle this when we project our data back to the larger CRC Seurat object and we will get an error message."
• Add more commentary on the interpretation of the UMAP and SpatialOverlay figures at the end of the lesson
• Add time estimate for running RCTD

Lesson 13 - DGE

• Create answer key solutions

Lesson 14 - SVGs

• Create question to run Moran's I on a different cell type and answer key solutions