-
When I run this code
ps
-
Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/mjemons/spatialFDA
Confirm the following by editi…
-
**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 automated p…
-
Hello,
I ran run_escape on a Single cell dataset processed in Seurat. I then normalized using performNormalization and used FindMarkers to find pathways specifically enriched in my cell type of int…
-
Hello,
I worked on developing a [function](https://github.com/LieberInstitute/visiumStitched/blob/devel/R/spe_to_seurat.R) to convert a `SpatialExperiment` object to a `Seurat` object, which, a…
-
Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/christinehou11/humanHippocampus2024
Confirm the f…
-
Hi,
thanks for the great package!
Since I last updated the R-version and packages etc. I get the problem that custom colors can't be mapped correctly in pbMDS.
```
pbMDS(sce, by = "cluster_id"…
-
Hi,
We noticed an issue between reading the `raw` and `filtered` outputs from SpaceRanger that I'm not sure whether `read10xVisium()` could address or not.
I incorrectly thought that the only di…
-
Hello,
Since fetch_data returns error on my machine, I manually downloaded data from the https link for `type == "sce"` in the fetch_data() function and converted the downloaded sce to spe using `…
-
**Describe the bug**
Currently, the [addClusters](https://www.archrproject.com/reference/addClusters.html) parameter 'method' which can be specified as Seurat or Scran, is the same parameter name as …