Thanks again for this package. It has been a huge benefit to our group!
Seurat's underlying data structure has changed substantially in version 5+ to support spatial data and other improvements. I have written a basic script for exporting data from a Seurat v5 object in a cellbrowser-friendly format and wanted to share in case you were looking to update your export script for v3: https://github.com/NUPulmonary/utils/blob/master/R/cellbrowser_export_seurat5.R.
For spatial, this generally requires merging FOVs into a single meta-FOV, which I've also written a helper function for: https://github.com/NUPulmonary/utils/blob/master/R/concatenate_fovs.R.
Feel free to mark as closed if this is low priority, but thought I would share. I would normally submit a PR but I am much less proficient in python.
Thanks much!
Thanks again for this package. It has been a huge benefit to our group!
Seurat's underlying data structure has changed substantially in version 5+ to support spatial data and other improvements. I have written a basic script for exporting data from a Seurat v5 object in a cellbrowser-friendly format and wanted to share in case you were looking to update your export script for v3: https://github.com/NUPulmonary/utils/blob/master/R/cellbrowser_export_seurat5.R.
For spatial, this generally requires merging FOVs into a single meta-FOV, which I've also written a helper function for: https://github.com/NUPulmonary/utils/blob/master/R/concatenate_fovs.R.
Feel free to mark as closed if this is low priority, but thought I would share. I would normally submit a PR but I am much less proficient in python.
Thanks much!