Skip to contents

Using the CellPhoneDB Database

Source: vignettes/articles/cellphonedb_vignette.Rmd
cellphonedb_vignette.Rmd

The dominoSignal analysis pipeline requires the use of a reference receptor - ligand database to identify potential receptor - ligand interactions. We recommend the use of CellPhoneDB. Here is a very brief tutorial on how to download the requisite files from CellPhoneDB v4.0.0.

File Downloads for CellPhoneDB:

Database files from CellPhoneDB v4.0.0 for human scRNAseq data can be installed from a public Github repository from the Tiechmann Group that developed CellPhoneDB.

# URL for desired version of CellPhoneDB
cellphone_url <- "https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz"

# download compressed database
cellphone_tar <- paste0(temp_dir, "/cellphoneDB_v4.tar.gz")
download.file(url = cellphone_url, destfile = cellphone_tar)

# move contents of the compressed file to a new directory
untar(tarfile = cellphone_tar, exdir = cellphone_dir)
cellphone_data <- paste0(cellphone_dir, "/cellphonedb-data-4.0.0/data")

To facilitate the use of these files in the format used in dominoSignal, we include a helper function, create_rl_map_cellphonedb(), that automatically parses files from the CellPhoneDB database to arrive at the rl_map format. For more information on how to use these files in the dominoSignal pipeline, please see our Getting Started page. To learn how to use SCENIC for TF activation scoring, please see our SCENIC for TF Activation Scoring tutorial.

Vignette Build Information

Date last built and session information:

Sys.Date()
#> [1] "2024-08-05"
sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.36     desc_1.4.3        R6_2.5.1          fastmap_1.2.0    
#>  [5] xfun_0.46         cachem_1.1.0      knitr_1.48        htmltools_0.5.8.1
#>  [9] rmarkdown_2.27    lifecycle_1.0.4   cli_3.6.3         sass_0.4.9       
#> [13] pkgdown_2.1.0     textshaping_0.4.0 jquerylib_0.1.4   systemfonts_1.1.0
#> [17] compiler_4.4.1    tools_4.4.1       ragg_1.3.2        bslib_0.8.0      
#> [21] evaluate_0.24.0   yaml_2.3.10       formatR_1.14      jsonlite_1.8.8   
#> [25] rlang_1.1.4       fs_1.6.4          htmlwidgets_1.6.4