-
-
Hello,
First of all, congratulations on what looks to be a very cool tool!
I was wondering if it was possible to run the tool on imaging based spatial data such as cosmx? From the preprint it se…
-
**DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT.**
**PLEASE POST THIS TEMPLATE UNCHANGED THEN FOLLOW ITS INSTRUCTIONS IN A NEW COMMENT**
# General Notes
This repository serves as a mostly automa…
-
1. spatial image
2. UMAP and violin plots
3. Focus on smaller region
4. ProjectR integration
1. This leads to visualizing cell types.
This is a list in flux
-
**Describe the bug**
I have a raster layer that is throwing a warning during Step 1 that I believe is causing a failure during Step 2. The warning, "Caught exception processing covariate: clay -- --…
-
Hi, thanks for the excellent repository of example data! Would you be interested in some spatial data / spatial models that demonstrate similar concepts as the classic Anscombe's quartet?
-
Hello, I am trying Seurat for the latest visium HD data and trying to use SpatialFeaturePlot function. I used the exact same script shown in vignette for preprocessing, but the feature plot is just H&…
-
Hi Jan,
I am using SPATA2 on a Xenium dataset .
I want to create a spatial trajectory in the image to view the spatial distribution of specified cell types.
But currently the ”createSpatialTrajecto…
-
Hello everyone,
I have a question about the ‘new’ TG part 2 on IACS, which is also published here in the technical-guildlines repository. In Germany, there is a group working on this topic in order…
-
Trying to use BPCells to help with smoother analysis of Visium HD data but keep getting errors.
localdir visium_data
> # Convert to BPCells format
> expr_matrix expr_matrix_int
> write_ma…