scKIM
Static AWS-hostable browser solution for scRNA-seq and spatial transcriptomics.
The goal is to use D3FC GPU-accelerated drawing and data streaming, drawing from data science visualization examples here and here to speed up presentation of 1M+ cells/spatial spots, and still achieving lowest entry and sharing threshold possible - a link in the browser without any additional software installations or dataset downloads.
Current working examples (AWS)
Current working examples (local)
Git clone the repo and open index.html. May need additional settings:
# macOS
open -a "Google Chrome" --args --allow-file-access-from-files
# linux
/usr/bin/chromium-browser --allow-file-access-from-files
# windows
add --allow-file-access-from-files to properties
Comparison to other browser solutions
| Consideration | ScKIM_D3 | cellBrowser | cellXgene | R shiny solutions | 10x Loupe |
|---|---|---|---|---|---|
| Web access | ✓ | ✓ | ✓ | ✓ | x |
| Amazon Cloud deployment | ✓ | ✓ | x | x | x |
| Spatial information | ✓ | x | ✓ | ✓ | ✓ |
| Custom data | ✓ | ✓ | ✓ | ✓ | x |
| Giant datasets | ✓ | ✓ | ✓ | x | ✓ |
| Differential expression analysis | x | x | ✓ | ✓ | ✓ |