To run the codes in Julia, python and R, the following tools need to be pre-installed in your workstation.
- CellScopes.jl:https://github.com/TheHumphreysLab/CellScopes.jl
- Cellpose:https://github.com/MouseLand/cellpose
- Baysor:https://github.com/kharchenkolab/Baysor
- Seurat:https://github.com/satijalab/seurat
- SpaGCN:https://github.com/jianhuupenn/SpaGCN
- Tangram:https://github.com/broadinstitute/Tangram
- Scanpy:https://github.com/scverse/scanpy
- SpaGE:https://github.com/tabdelaal/SpaGE
- gimVI:https://github.com/scverse/scvi-tools
- STdeconvolve: https://github.com/JEFworks-Lab/STdeconvolve
- TACCO: https://github.com/simonwm/tacco
- RCTD: https://github.com/dmcable/spacexr
- Spotlight: https://github.com/MarcElosua/SPOTlight