Session information

All R-package dependencies for the current Asc-Seurat release are declared in DESCRIPTION. Follow the upstream BPCells R installation instructions first so the HDF5 system dependency is available, then install BPCells before installing Asc-Seurat:

install.packages(c("pak", "remotes"))
remotes::install_github("bnprks/BPCells/r", upgrade = "never")
pak::pkg_install(
  "Pereira-Lab-UF/asc_seurat",
  dependencies = c("Depends", "Imports", "LinkingTo")
)

This explicit BPCells step avoids a known pak failure with the GitHub sub-directory package used by BPCells. The explicit dependencies value installs every package declared as an app runtime dependency in DESCRIPTION, including PseudotimeDE; it avoids only developer, documentation, and test-only packages. On macOS, PseudotimeDE requires the official R GNU Fortran toolchain from R for macOS tools.

To capture the exact versions on your machine for a methods section or a bug report, run sessionInfo() after launching the app:

ascseurat::run_app()
# … in another R session, or after closing the app:
sessionInfo()

See References for the list of packages Asc-Seurat directly calls.