List the cell type annotation tools supported by RunCellTypeAnnotation()

List the cell type annotation tools supported by RunCellTypeAnnotation()

Usage

celltype_annotation_tools(name = NULL)

Arguments

name

The name(s) of the tool(s) to look up. If NULL (default), all supported tools are returned.

Value

A named list of the tools selected by name, each with:

• level: "cluster" or "cell", the level the tool natively annotates at.

• h5ad: TRUE when the tool needs the object converted to AnnData (python-based tools, omitted otherwise).

Examples

names(celltype_annotation_tools())
#>  [1] "hitype"         "sctype"         "sccatch"        "celltypist"    
#>  [5] "scsorter"       "scina"          "garnett"        "singler"       
#>  [9] "schdeepinsight" "llmcelltype"    "cellassign"     "scbert"        
#> [13] "scagenttype"    "cellid"         "direct"         "cell"          
#> [17] "ucell"          "aucell"         "gsva"           "singscore"     
#> [21] "scmap"          "cheetah"        "scclassify"     "scpred"        
#> [25] "mapquery"       "azimuth"        "scsa"           "maca"          
#> [29] "scmapnet"       "mllmcelltype"   "lict"          
celltype_annotation_tools("direct")
#> $direct
#> $direct$level
#> [1] "cluster"
#> 
#>