# Python side
scanpy>=1.10
anndata
scipy
# R side (install separately on the server):
#   R >= 4.2 with monocle3 (+ Matrix, jsonlite). monocle3 is installed from
#   GitHub and pulls a heavy spatial/stats R stack that needs SYSTEM LIBRARIES.
#   Validated install (macOS; apt-get equivalents on Linux):
#     brew install gdal geos proj udunits nlopt cmake     # for terra/sf/units/nloptr
#     Rscript -e 'install.packages(c("terra","units","nloptr","sf","lme4","spdep"))'
#     Rscript -e 'BiocManager::install(c("SingleCellExperiment","batchelor","leidenbase","ggrastr"))'
#     Rscript -e 'remotes::install_github("cole-trapnell-lab/monocle3")'
#   Rscript must be on PATH (or set RSCRIPT_BIN).
#   Validated end-to-end on the pancreas dataset: roots at Ngn3-low EP and recovers
#   the endocrine pseudotime ordering (Ngn3 low EP -> Ngn3 high EP -> Fev+ ->
#   Delta/Epsilon/Beta/Alpha).
