Modern spatial transcriptomics techniques can reach ever-finer resolutions, and their resulting data makes it possible to investigate the cellular interaction spaces between different tissues. In particular, the dynamics of these interaction spaces are well suited to the concept of RNA velocity. Here, we present a pipeline to map RNA velocities of these interaction spaces.
Scripts 1_deconvolution.R and 2_detect_markers.R run the RCTD and Seurat sections, and need to be run in that sequence.
After velocyto has also been run, 3_velocity.py can be used to map velocities.
compare_markers.R and plot_overviews.R are miscellaneous scripts to generate statistics and plots.