Davide Risso

Hi @lambdamoses , thanks for reporting this. @LTLA is this the intended behavior? I would imagine that each object should have only one version, but on the other hand, can...

Hi @FionaMoon , I cannot reproduce this on my end. Would you mind sharing the results of `sessionInfo()` and confirm that `BiocManager::valid()` returns TRUE?

I've tried on a vanilla R session the following and it throws an error as expected. ```{r} library(SingleCellExperiment) example(SingleCellExperiment) sce1 = sce assays(sce1) = assays(sce1)[1] sce2 = sce assays(sce2) =...

My two cents: I think it's very valuable to have a dedicated IO package specific to spatial data and each different technology (current and future). I would not bind it...

But isn't this what [SpatialFeatureExperiment](https://www.bioconductor.org/packages/release/bioc/html/SpatialFeatureExperiment.html) is doing?

Thanks @estellad and @lmweber ! I think this is a good plan. I second @lgeistlinger 's suggestion for the package name and for storing (optionally) polygons as terra objects in...

zinbwave uses BiocParallel for parallel computations and BiocParallel has some issues with MulticoreParam, I found that using DoparParam() instead improves things greatly.

Thanks @HenrikBengtsson for the comment. Note that `zinbwave` is kind of agnostic to the parallelization back-end and relies completely on `BiocParallel`. All the zinbwave functions that support parallelization default to...

Hi @HenrikBengtsson it is indeed useful to know this bad behavior of the RStudio/multicore combination. @mtmorgan I suspect that some of my code is in the `bad()` form, but I...

Hi @reubenthomas , internally, a lot of the zinbwave functions have features in columns and genes in rows, hence, we developed these functions thinking in the same manner. But you're...