Aaron Lun

Hard to know exactly what I was thinking then, but it was probably along these lines: if we wanted a pure C implementation, we would mimic C++ templates with macros...

It really depends on what your labels are. If your labels are coarse entities like "T cell" and "B cell", I would tell you not to worry about it and...

Biologically. To be more specific, I would expect that most perturbations would not change how different broad cell types are defined. (Individual cells can of course shift between cell types,...

> If the drug or disease indeed triggers differentiation, does the multi reference strategy still work? Differentiation is not the concern here. You need to ask yourself how the cell...

Nothing too complicated. When `de.method="wilcox"` or `"t"`, the package uses **scran**'s functions to perform the pairwise t-tests or Wilcoxon tests in an efficient manner; so to use that functionality, you'll...

Hm. Traditionally I have always considered the error message out of `::` to be satisfactory. Also it was a pain to have to write these protective clauses every time I...

**BiocManager** seems like the best place for this to live. The package has minimal dependencies and it must be installed by default before **SingleR** anyway, so I wouldn't consider it...

I dunno who Christoph is, but see #98.

I have no idea; never seen this error before. I'm guessing that `nrow()` on your test dataset is returning `NULL`, leading to the observed error message. If you can create...

You should look at what `GetAssayData` produces. `SingleR` is expecting some kind of matrix, e.g., ordinary matrix, `dgCMatrix`.