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 Under development (unstable) (2025-03-13 r87965)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.21-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_1.7.6 shiny_1.10.0        BiocStyle_2.35.0   
#> 
#> loaded via a namespace (and not attached):
#>  [1] rappdirs_0.3.3          sass_0.4.9              generics_0.1.3         
#>  [4] BiocVersion_3.21.1      RSQLite_2.3.9           digest_0.6.37          
#>  [7] magrittr_2.0.3          evaluate_1.0.3          bookdown_0.42          
#> [10] fastmap_1.2.0           blob_1.2.4              AnnotationHub_3.15.0   
#> [13] jsonlite_2.0.0          AnnotationDbi_1.69.1    GenomeInfoDb_1.43.4    
#> [16] DBI_1.2.3               promises_1.3.2          BiocManager_1.30.25    
#> [19] httr_1.4.7              UCSC.utils_1.3.1        Biostrings_2.75.4      
#> [22] codetools_0.2-20        jquerylib_0.1.4         cli_3.6.4              
#> [25] crayon_1.5.3            rlang_1.1.5             XVector_0.47.2         
#> [28] dbplyr_2.5.0            Biobase_2.67.0          bit64_4.6.0-1          
#> [31] cachem_1.1.0            yaml_2.3.10             tools_4.6.0            
#> [34] memoise_2.0.1           dplyr_1.1.4             GenomeInfoDbData_1.2.14
#> [37] filelock_1.0.3          httpuv_1.6.15           ExperimentHub_2.15.0   
#> [40] BiocGenerics_0.53.6     curl_6.2.2              png_0.1-8              
#> [43] vctrs_0.6.5             R6_2.6.1                mime_0.13              
#> [46] stats4_4.6.0            lifecycle_1.0.4         BiocFileCache_2.15.1   
#> [49] KEGGREST_1.47.1         IRanges_2.41.3          S4Vectors_0.45.4       
#> [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_4.6.0