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.
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
| 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 | ✓ | ✓ | ✓ |