Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2025-11-26 05:46:22.741181
Compiled: Wed Dec 10 06:01:41 2025

1 Installation

To install this package, start R (>= 4.1.0) and enter:

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("AHLRBaseDbs")

2 Fetch LRBaseDb databases from AnnotationHub

The AHLRBaseDbs package provides the metadata for all LRBaseDb SQLite databases in AnnotationHub. First we load/update the AnnotationHub resource.

library(AnnotationHub)
ah <- AnnotationHub()

Next we list all LRBaseDb entries from AnnotationHub.

query(ah, "LRBaseDb")
## AnnotationHub with 256 records
## # snapshotDate(): 2025-11-14
## # $dataprovider: FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CE...
## # $species: Xenopus tropicalis, Vulpes vulpes, Vombatus ursinus, Ursus marit...
## # $rdataclass: SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## #   rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["AH121497"]]' 
## 
##              title                                                         
##   AH121497 | LRBaseDb for Anolis carolinensis (Anole lizard, v009)         
##   AH121498 | LRBaseDb for Aquila chrysaetos chrysaetos (Golden eagle, v009)
##   AH121499 | LRBaseDb for Astatotilapia calliptera (Eastern happy, v009)   
##   AH121500 | LRBaseDb for Ailuropoda melanoleuca (Panda, v009)             
##   AH121501 | LRBaseDb for Apis mellifera (Honey bee, v009)                 
##   ...        ...                                                           
##   AH121867 | LRBaseDb for Tursiops truncatus (Dolphin, v010)               
##   AH121868 | LRBaseDb for Ursus maritimus (Polar bear, v010)               
##   AH121869 | LRBaseDb for Vombatus ursinus (Common wombat, v010)           
##   AH121870 | LRBaseDb for Vulpes vulpes (Red fox, v010)                    
##   AH121871 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v010)

We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket with mcols().

mcols(query(ah, "LRBaseDb"))
## DataFrame with 256 rows and 15 columns
##                           title           dataprovider                species
##                     <character>            <character>            <character>
## AH121497 LRBaseDb for Anolis .. FANTOM5,DLRP,IUPHAR,..    Anolis carolinensis
## AH121498 LRBaseDb for Aquila .. FANTOM5,DLRP,IUPHAR,.. Aquila chrysaetos ch..
## AH121499 LRBaseDb for Astatot.. FANTOM5,DLRP,IUPHAR,.. Astatotilapia callip..
## AH121500 LRBaseDb for Ailurop.. FANTOM5,DLRP,IUPHAR,.. Ailuropoda melanoleuca
## AH121501 LRBaseDb for Apis me.. FANTOM5,DLRP,IUPHAR,..         Apis mellifera
## ...                         ...                    ...                    ...
## AH121867 LRBaseDb for Tursiop.. FANTOM5,DLRP,IUPHAR,..     Tursiops truncatus
## AH121868 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH121869 LRBaseDb for Vombatu.. FANTOM5,DLRP,IUPHAR,..       Vombatus ursinus
## AH121870 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH121871 LRBaseDb for Xenopus.. FANTOM5,DLRP,IUPHAR,..     Xenopus tropicalis
##          taxonomyid      genome            description coordinate_1_based
##           <integer> <character>            <character>          <integer>
## AH121497      28377          NA Correspondence table..                  1
## AH121498     223781          NA Correspondence table..                  1
## AH121499       8154          NA Correspondence table..                  1
## AH121500       9646          NA Correspondence table..                  1
## AH121501       7460          NA Correspondence table..                  1
## ...             ...         ...                    ...                ...
## AH121867       9739          NA Correspondence table..                  1
## AH121868      29073          NA Correspondence table..                  1
## AH121869      29139          NA Correspondence table..                  1
## AH121870       9627          NA Correspondence table..                  1
## AH121871       8364          NA Correspondence table..                  1
##                      maintainer rdatadateadded preparerclass
##                     <character>    <character>   <character>
## AH121497 Koki Tsuyuzaki <k.t...     2025-04-08   AHLRBaseDbs
## AH121498 Koki Tsuyuzaki <k.t...     2025-04-08   AHLRBaseDbs
## AH121499 Koki Tsuyuzaki <k.t...     2025-04-08   AHLRBaseDbs
## AH121500 Koki Tsuyuzaki <k.t...     2025-04-08   AHLRBaseDbs
## AH121501 Koki Tsuyuzaki <k.t...     2025-04-08   AHLRBaseDbs
## ...                         ...            ...           ...
## AH121867 Koki Tsuyuzaki <k.t...     2025-10-17   AHLRBaseDbs
## AH121868 Koki Tsuyuzaki <k.t...     2025-10-17   AHLRBaseDbs
## AH121869 Koki Tsuyuzaki <k.t...     2025-10-17   AHLRBaseDbs
## AH121870 Koki Tsuyuzaki <k.t...     2025-10-17   AHLRBaseDbs
## AH121871 Koki Tsuyuzaki <k.t...     2025-10-17   AHLRBaseDbs
##                                                     tags  rdataclass
##                                                   <AsIs> <character>
## AH121497 Annotation,Anole lizard,Anolis carolinensis,...  SQLiteFile
## AH121498  Annotation,Aquila chrysaetos ch..,BADERLAB,...  SQLiteFile
## AH121499  Annotation,Astatotilapia callip..,BADERLAB,...  SQLiteFile
## AH121500  Ailuropoda melanoleuca,Annotation,BADERLAB,...  SQLiteFile
## AH121501          Annotation,Apis mellifera,BADERLAB,...  SQLiteFile
## ...                                                  ...         ...
## AH121867                 Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH121868                 Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH121869                 Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH121870                 Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH121871                 Annotation,BADERLAB,BIOMART,...  SQLiteFile
##                       rdatapath              sourceurl  sourcetype
##                     <character>            <character> <character>
## AH121497 AHLRBaseDbs/v009/LRB.. https://github.com/r..         CSV
## AH121498 AHLRBaseDbs/v009/LRB.. https://github.com/r..         CSV
## AH121499 AHLRBaseDbs/v009/LRB.. https://github.com/r..         CSV
## AH121500 AHLRBaseDbs/v009/LRB.. https://github.com/r..         CSV
## AH121501 AHLRBaseDbs/v009/LRB.. https://github.com/r..         CSV
## ...                         ...                    ...         ...
## AH121867 AHLRBaseDbs/v010/LRB.. https://github.com/r..         CSV
## AH121868 AHLRBaseDbs/v010/LRB.. https://github.com/r..         CSV
## AH121869 AHLRBaseDbs/v010/LRB.. https://github.com/r..         CSV
## AH121870 AHLRBaseDbs/v010/LRB.. https://github.com/r..         CSV
## AH121871 AHLRBaseDbs/v010/LRB.. https://github.com/r..         CSV

We can query only the LRBaseDb SQLite files for species Mus musculus.

qr <- query(ah, c("LRBaseDb", "Mus musculus"))
# filepath_mmu <- qr[[1]]

This filepath is can be specified with the argument of RSQLite::dbConnect and LRBaseDbi::LRBaseDb and also used as the argument of scTensor, which is an R/Bioconductor package for the detection of cell-cell interaction detection.

For the details, check the vignettes of RSQLite, LRBaseDbi, and scTensor.

Session information

## R Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_4.1.0 BiocFileCache_3.1.0 dbplyr_2.5.1       
## [4] BiocGenerics_0.57.0 generics_0.1.4      BiocStyle_2.39.0   
## 
## loaded via a namespace (and not attached):
##  [1] rappdirs_0.3.3       sass_0.4.10          BiocVersion_3.23.1  
##  [4] RSQLite_2.4.5        digest_0.6.39        magrittr_2.0.4      
##  [7] evaluate_1.0.5       bookdown_0.46        fastmap_1.2.0       
## [10] blob_1.2.4           jsonlite_2.0.0       AnnotationDbi_1.73.0
## [13] DBI_1.2.3            BiocManager_1.30.27  httr_1.4.7          
## [16] purrr_1.2.0          Biostrings_2.79.2    httr2_1.2.2         
## [19] jquerylib_0.1.4      cli_3.6.5            crayon_1.5.3        
## [22] rlang_1.1.6          XVector_0.51.0       Biobase_2.71.0      
## [25] bit64_4.6.0-1        withr_3.0.2          cachem_1.1.0        
## [28] yaml_2.3.11          otel_0.2.0           tools_4.6.0         
## [31] memoise_2.0.1        dplyr_1.1.4          filelock_1.0.3      
## [34] curl_7.0.0           png_0.1-8            vctrs_0.6.5         
## [37] R6_2.6.1             stats4_4.6.0         lifecycle_1.0.4     
## [40] Seqinfo_1.1.0        KEGGREST_1.51.1      S4Vectors_0.49.0    
## [43] IRanges_2.45.0       bit_4.6.0            pkgconfig_2.0.3     
## [46] pillar_1.11.1        bslib_0.9.0          glue_1.8.0          
## [49] xfun_0.54            tibble_3.3.0         tidyselect_1.2.1    
## [52] knitr_1.50           htmltools_0.5.9      rmarkdown_2.30      
## [55] compiler_4.6.0