Constantin

Okay, I decided that I am fine for now with densifying each column if `colQuantiles()` is called with a non-default `type` argument. I opened a PR at https://github.com/Bioconductor/MatrixGenerics/pull/14 to include...

I also realized why `preserveShape` cannot be in the generic signature of `colRanks`: If the generic would look like this: ```{r} setGeneric("colRanks", function(x, rows = NULL, cols = NULL, ties.method...

Good point, but I worry that this would be even more surprising.

Hi Hervé, I understood Henrik in https://github.com/HenrikBengtsson/matrixStats/issues/183 that center must be an honest center estimate of the column means: > This calculation is based on the assumption that center is...

Hi Christoph, thanks for the report. Yes, you are right, adding an `as.matrix()` somewhere should fix the issue. However, the deeper issue is that `MatrixGenerics` apparently doesn't yet realize that...

My C++ is templated to either use `int` or `double` depending on the type of the input matrix (e.g., https://github.com/const-ae/glmGamPoi/blob/master/src/beta_estimation.cpp#L431). But I have never tested it with gigantic counts, but...

A quick experiment seems to confirm that `glmGamPoi` can handle counts which are larger than `.Machine$integer.max`: ``` r # Integers with values larger than 2^31-1 = 2,147,483,647 = 2.1 *...

Hi Anna, this looks like a cool effort. I just skimmed your section on "Normalization" and wanted to point to a benchmark article, I recently wrote https://www.biorxiv.org/content/10.1101/2021.06.24.449781v4. We compared many...

I agree with Gregor that the easiest change might be to simply allow some way to provide a design matrix and then just skip the step `build_design_matrix` at https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/dds.py#L249. Of...

Hi Sarah, Yes, you can use LEMUR for differential state analysis! If you are particularly interested in the gene expression changes occurring in B cells, you would run LEMUR only...