Get available CellTypist models

Unified CellTypist model management interface. Use it to list available models, download models, inspect model metadata, extract model markers, subset models, convert models, or delete local models. Model listing and file-management examples are non-executing because they may download or modify local files.

Usage

CellTypistModels(
  action = c("list", "download", "info", "markers", "subset", "convert", "delete"),
  on_the_fly = FALSE,
  model = NULL,
  force_update = FALSE,
  cell_type = NULL,
  top_n = 10,
  only_positive = TRUE,
  keep_cell_types = NULL,
  exclude_cell_types = NULL,
  output_model_path = NULL,
  map_file = NULL,
  sep = ",",
  convert_from = NULL,
  convert_to = NULL,
  unique_only = TRUE,
  collapse = c("average", "random"),
  random_state = 0,
  verbose = TRUE
)

Arguments

action: Action to perform. One of "list", "download", "info", "markers", "subset", "convert", or "delete".
on_the_fly: If TRUE, only show downloaded models. If FALSE, show all available models (fetch list from server). Used when action = "list". Default is FALSE.
model: Model name(s) used for actions other than "list".
force_update: Whether to refresh the model index before downloading. Used when action = "download".
cell_type: Cell type used when action = "markers".
top_n: Number of markers to extract when action = "markers".
only_positive: Whether to return only positive markers.
keep_cell_types: Cell types retained when action = "subset".
exclude_cell_types: Cell types removed when action = "subset".
output_model_path: Optional output path used by "subset" or "convert". If NULL, the original model file will be overwritten.
map_file: Optional two-column gene mapping file used by action = "convert".
sep: Delimiter used by map_file.
convert_from, convert_to: Column indices used by map_file.
unique_only: Whether to use only one-to-one mappings in action = "convert".
collapse: How to collapse one-to-many mappings in action = "convert".
random_state: Random seed used when collapse = "random".
verbose: Whether to print the message. Default is TRUE.

Value

Depends on action: a data frame, a summary list, or a character vector.

Examples

if (FALSE) { # \dontrun{
check_python("celltypist")
models <- CellTypistModels(action = "list", on_the_fly = TRUE)
head(models)
CellTypistModels(action = "info", model = "Immune_All_Low.pkl")
} # }

Usage

Arguments

Value

See also

Examples