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I was using R version 4.2.0, SpatialExperiment version 1.6.0, and spatialLIBD version 1.8.3. I think the latest version of R is 4.2.1 but I believe the package versions are current
I'll try using this other Shiny app quickly and let you know what I find! Thanks!
I went on the lymph node app (EDIT: https://libd.shinyapps.io/spatialLIBD_Human_Lymph_Node_10x/) and successfully generated this csv file: spatialLIBD_ManualAnnotation_2022-07-05_17-57-08.csv
It's just two square regions of the tissue, annotated test1 or test2. After I made these, I closed the app and started a new session. When I try to upload the csv to the Shiny app, it doesn't seem to work, as all spots are categorized as NA and none as test1 or test2. So, I think this may be an bug with the current version of spatialLIBD or a dependency/dependencies and not the HPC app
The text was updated successfully, but these errors were encountered:
First reported by @Erik-D-Nelson at https://jhu-genomics.slack.com/archives/C03KD30V3ST/p1657043593610579
The text was updated successfully, but these errors were encountered: