List bundled Shennong signatures

Usage

sn_list_signatures(species = NULL, include_groups = FALSE)

Arguments

species: Optional species filter. Use NULL to return all species.
include_groups: If TRUE, include non-leaf group nodes from the signature tree.

Value

A tibble with the available signature paths, node kinds, and gene counts.

Examples

sn_list_signatures(species = "human")
#> # A tibble: 15 × 5
#>    species path                         name               kind      n_genes
#>    <chr>   <chr>                        <chr>              <chr>       <int>
#>  1 human   Blocklists/Pseudogenes       Pseudogenes        signature   12600
#>  2 human   Blocklists/Non-coding        Non-coding         signature    7783
#>  3 human   Programs/HeatShock           HeatShock          signature      97
#>  4 human   Programs/cellCycle.G1S       cellCycle.G1S      signature      42
#>  5 human   Programs/cellCycle.G2M       cellCycle.G2M      signature      52
#>  6 human   Programs/IFN                 IFN                signature     107
#>  7 human   Programs/Tcell.cytotoxicity  Tcell.cytotoxicity signature       3
#>  8 human   Programs/Tcell.exhaustion    Tcell.exhaustion   signature       5
#>  9 human   Programs/Tcell.stemness      Tcell.stemness     signature       4
#> 10 human   Programs/M1_macrophage       M1_macrophage      signature      54
#> 11 human   Programs/M2_macrophage       M2_macrophage      signature      43
#> 12 human   Compartments/Mito            Mito               signature      37
#> 13 human   Compartments/Ribo            Ribo               signature     168
#> 14 human   Compartments/TCR             TCR                signature     227
#> 15 human   Compartments/Immunoglobulins Immunoglobulins    signature     411
sn_list_signatures(species = "human", include_groups = TRUE)
#> # A tibble: 19 × 5
#>    species path                         name               kind      n_genes
#>    <chr>   <chr>                        <chr>              <chr>       <int>
#>  1 human   Blocklists                   Blocklists         group           0
#>  2 human   Blocklists/Pseudogenes       Pseudogenes        signature   12600
#>  3 human   Blocklists/Non-coding        Non-coding         signature    7783
#>  4 human   Programs                     Programs           group           0
#>  5 human   Programs/HeatShock           HeatShock          signature      97
#>  6 human   Programs/cellCycle.G1S       cellCycle.G1S      signature      42
#>  7 human   Programs/cellCycle.G2M       cellCycle.G2M      signature      52
#>  8 human   Programs/IFN                 IFN                signature     107
#>  9 human   Programs/Tcell.cytotoxicity  Tcell.cytotoxicity signature       3
#> 10 human   Programs/Tcell.exhaustion    Tcell.exhaustion   signature       5
#> 11 human   Programs/Tcell.stemness      Tcell.stemness     signature       4
#> 12 human   Programs/M1_macrophage       M1_macrophage      signature      54
#> 13 human   Programs/M2_macrophage       M2_macrophage      signature      43
#> 14 human   Cell_types                   Cell_types         group           0
#> 15 human   Compartments                 Compartments       group           0
#> 16 human   Compartments/Mito            Mito               signature      37
#> 17 human   Compartments/Ribo            Ribo               signature     168
#> 18 human   Compartments/TCR             TCR                signature     227
#> 19 human   Compartments/Immunoglobulins Immunoglobulins    signature     411