TODOs

[mblue9]

Keeping track of what we still need to do

• update slides @stemangiola
• change Seurat commands to Bioc @stemangiola
• add explanation for map/map2 etc @mblue9
• adjust slides e.g. remove single cell pic @stemangiola
• try fix actions for tidy packages @mblue9 (just tidybulk not passing yet)
• review info in email I sent Jul 22 @stemangiola
• edits to workshop from today's meeting @mblue9
• replace tidyfeaturomics in tidySingleCellExperiment website
• investigate why base R code block different to tidy
• fix restore_SingleCellExperiment_show options("restore_SingleCellExperiment_show" = FALSE)` doesn't work? #17 @stemangiola

[mblue9]

For investigate why base R code block different to tidy the difference is because the base R code was using the raw counts assay while tidy join_features uses the logcounts assay.

I've changed the base R code to use logcounts here (if that's not right let me know).

Noticed that there doesn't seem to be a way to use the raw counts with tidySCE join_features here, or to specify which assay to use if multiple present, so opened issue in tidySCE to note that. It's not something that has to be fixed before workshop I think.

[stemangiola]

Noticed that there doesn't seem to be a way to use the raw counts with tidySCE join_features here, or to specify which assay to use if multiple present, so opened issue in tidySCE to note that. It's not something that has to be fixed before workshop I think.

join_features should have an assay argument assay="counts"

[mblue9]

Ah perfect that works 👍 I'll close the other issue.