Analyses associated with https://doi.org/10.1101/2021.09.20.461129

For full analyses and reproducible runs, see https://doi.org/10.24433/CO.0051950.v1

Code base for running simulation analyses (clone, install packages if necessary, and set appropriate "sim_repo_path" variable in "time_simulation" notebooks): https://github.com/hmbaghdassarian/c2c_sim

Environment: associated environments include 1) simulation analyses (reproduced via instructions in c2c_sim repo) and 2) cellchat analyses (reproduced by instructions in "notebooks/cellchat_benchmark/env_setup/README.md"). These environments can likely be combined as in the CodeOcean capsule, but has not been tried locally.

Note to self: environments are named 1) "cci_dt" and 2) "cellchat" respectively.