Get ligand-receptor database

Load built-in ligand-receptor interaction databases for cell-cell communication analysis.

Usage

ligand_receptor_database(
  database = c("CellChat", "CellPhoneDB"),
  species = c("mouse", "human", "zebrafish"),
  signaling_type = "Secreted Signaling"
)

Arguments

database

Database name: "CellChat" (default) or "CellPhoneDB".

species

Species: "mouse" (default), "human", or "zebrafish" (CellChat only).

signaling_type

Type of signaling to include: "Secreted Signaling" (default), "Cell-Cell Contact", "ECM-Receptor" (CellChat), or NULL for all.

Value

A data frame with columns:

ligand

Ligand gene name(s), underscore-separated for complexes

receptor

Receptor gene name(s), underscore-separated for complexes

pathway

Signaling pathway name

signaling_type

Type of signaling interaction

References

CellChat: Jin, S. et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun 12, 1088 (2021).

CellPhoneDB: Efremova, M. et al. CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc 15, 1484-1506 (2020).

Examples

# Load mouse secreted signaling from CellChat
df_lr <- ligand_receptor_database("CellChat", "mouse", "Secreted Signaling")
head(df_lr)
#>   ligand      receptor pathway     signaling_type
#> 1  Tgfb1 Tgfbr1_Tgfbr2    TGFb Secreted Signaling
#> 2  Tgfb2 Tgfbr1_Tgfbr2    TGFb Secreted Signaling
#> 3  Tgfb3 Tgfbr1_Tgfbr2    TGFb Secreted Signaling
#> 4  Tgfb1 Acvr1b_Tgfbr2    TGFb Secreted Signaling
#> 5  Tgfb1 Acvr1c_Tgfbr2    TGFb Secreted Signaling
#> 6  Tgfb2 Acvr1b_Tgfbr2    TGFb Secreted Signaling

# Load all human CellChat interactions
df_lr_all <- ligand_receptor_database("CellChat", "human", NULL)