ludvigla

Adding additional columns to the Seurat object should not be an issue as long as you don't modify the spot labels, the number of spots or the order of spots....

One solution is to set the `useDingbats` option to `TRUE` in the pdf device. Here's a small example I tried on a mouse brain tissue data set: ``` p

You should be able to follow the [Seurat spatial vignette](https://satijalab.org/seurat/articles/spatial_vignette.html) to obtain cell type prediction scores. ```# cells this speeds up SCTransform dramatically with no loss in performance [library](https://rdrr.io/r/base/library.html)([dplyr](https://dplyr.tidyverse.org/)) singlecell_reference...

Hi Quanc, I'm working on a new package (which is not yet public) which will be an include quite a few new features. I will try to include this type...

Hi, Sorry for the inconvenience but there is a simple explanation for the discrepancy. The expression matrices were filtered to remove spots with 0 observed expression while the spotfiles contain...

Hi @krigia, Could you please elaborate a little? If the goal is simply to calculate an enrichment score based on a gene set there are some options available. You could...

Hi, If you wish to manually select spots, you can use the `ManualAnnotation` function. `se

Hi @mimisikai, The coordinates you are using are not the same ones used by `ST.FeaturePlot`. It uses either the `pixel_x`, `pixel_y` coordinates or `warped_x`, `warped_x` coordinates if the images have...

We will no longer maintain this package so we have no plan to upload it to conda. You can check out our new package `semla` available here: https://github.com/ludvigla/semla /Ludvig

This is likely an issue related to your installation of `magick`. Can you load and process images without issues using `magick`? https://cran.r-project.org/web/packages/magick/vignettes/intro.html