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 (2025-04-11)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.22-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] BiocHubsShiny_1.9.1 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_0.1.4      
#>  [4] BiocVersion_3.22.0   RSQLite_2.3.11       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_3.99.5
#> [13] jsonlite_2.0.0       AnnotationDbi_1.71.0 GenomeInfoDb_1.45.3 
#> [16] DBI_1.2.3            promises_1.3.2       BiocManager_1.30.25 
#> [19] httr_1.4.7           UCSC.utils_1.5.0     Biostrings_2.77.1   
#> [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] filelock_1.0.3       httpuv_1.6.16        ExperimentHub_2.99.5
#> [40] BiocGenerics_0.55.0  curl_6.2.2           png_0.1-8           
#> [43] vctrs_0.6.5          R6_2.6.1             mime_0.13           
#> [46] stats4_4.5.0         lifecycle_1.0.4      BiocFileCache_2.99.5
#> [49] KEGGREST_1.49.0      IRanges_2.43.0       S4Vectors_0.47.0    
#> [52] bit_4.6.0            pkgconfig_2.0.3      bslib_0.9.0         
#> [55] pillar_1.10.2        later_1.4.2          glue_1.8.0          
#> [58] Rcpp_1.0.14          xfun_0.52            tibble_3.2.1        
#> [61] tidyselect_1.2.1     knitr_1.50           xtable_1.8-4        
#> [64] htmltools_0.5.8.1    rmarkdown_2.29       compiler_4.5.0