1 BiocHubsShiny

The BiocHubsShiny package allows users to visually explore the AnnotationHub and ExperimentHub resources via shiny. It provides a tabular display of the available resources with the ability to filter and search through the column fields.

2 Installation

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

BiocManager::install("BiocHubsShiny")

3 Loading the package

library(BiocHubsShiny)

4 Display of resources

Resources are displayed interactively using the eponymous function:

BiocHubsShiny()

5 Filtering

You can filter by any of the columns in the table. For example, you can search for ‘Mus musculus’ to get resources only for that species:

6 Selection

Click on the rows to select the resources. They will show up as highlighted rows.

7 Import

Once the selection is highlighted, the code at the bottom of the app will be updated to show the commands for entering (reproducibly) into the R session.

8 Session Info

sessionInfo()
#> R version 4.5.0 Patched (2025-04-21 r88169)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Ventura 13.7.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] BiocHubsShiny_1.9.0 shiny_1.10.0        BiocStyle_2.37.0   
#> 
#> loaded via a namespace (and not attached):
#>  [1] rappdirs_0.3.3          sass_0.4.10             generics_0.1.3         
#>  [4] BiocVersion_3.22.0      RSQLite_2.3.9           digest_0.6.37          
#>  [7] magrittr_2.0.3          evaluate_1.0.3          bookdown_0.43          
#> [10] fastmap_1.2.0           blob_1.2.4              AnnotationHub_3.99.0   
#> [13] jsonlite_2.0.0          AnnotationDbi_1.71.0    GenomeInfoDb_1.45.0    
#> [16] DBI_1.2.3               promises_1.3.2          BiocManager_1.30.25    
#> [19] httr_1.4.7              UCSC.utils_1.5.0        Biostrings_2.77.0      
#> [22] codetools_0.2-20        httr2_1.1.2             jquerylib_0.1.4        
#> [25] cli_3.6.5               crayon_1.5.3            rlang_1.1.6            
#> [28] XVector_0.49.0          dbplyr_2.5.0            Biobase_2.69.0         
#> [31] bit64_4.6.0-1           cachem_1.1.0            yaml_2.3.10            
#> [34] tools_4.5.0             memoise_2.0.1           dplyr_1.1.4            
#> [37] GenomeInfoDbData_1.2.14 filelock_1.0.3          httpuv_1.6.16          
#> [40] ExperimentHub_2.99.0    BiocGenerics_0.55.0     curl_6.2.2             
#> [43] png_0.1-8               vctrs_0.6.5             R6_2.6.1               
#> [46] mime_0.13               stats4_4.5.0            lifecycle_1.0.4        
#> [49] BiocFileCache_2.99.0    KEGGREST_1.49.0         IRanges_2.43.0         
#> [52] S4Vectors_0.47.0        bit_4.6.0               pkgconfig_2.0.3        
#> [55] bslib_0.9.0             pillar_1.10.2           later_1.4.2            
#> [58] glue_1.8.0              Rcpp_1.0.14             xfun_0.52              
#> [61] tibble_3.2.1            tidyselect_1.2.1        knitr_1.50             
#> [64] xtable_1.8-4            htmltools_0.5.8.1       rmarkdown_2.29         
#> [67] compiler_4.5.0