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) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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
## 
## 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_1.7.1 shiny_1.9.1         BiocStyle_2.35.0   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.47.0         xfun_0.49               bslib_0.8.0            
##  [4] Biobase_2.67.0          vctrs_0.6.5             tools_4.5.0            
##  [7] generics_0.1.3          stats4_4.5.0            curl_6.0.0             
## [10] tibble_3.2.1            fansi_1.0.6             AnnotationDbi_1.69.0   
## [13] RSQLite_2.3.7           blob_1.2.4              pkgconfig_2.0.3        
## [16] dbplyr_2.5.0            S4Vectors_0.45.0        lifecycle_1.0.4        
## [19] GenomeInfoDbData_1.2.13 compiler_4.5.0          Biostrings_2.75.1      
## [22] httpuv_1.6.15           GenomeInfoDb_1.43.0     htmltools_0.5.8.1      
## [25] sass_0.4.9              yaml_2.3.10             later_1.3.2            
## [28] pillar_1.9.0            crayon_1.5.3            jquerylib_0.1.4        
## [31] cachem_1.1.0            mime_0.12               ExperimentHub_2.15.0   
## [34] AnnotationHub_3.15.0    tidyselect_1.2.1        digest_0.6.37          
## [37] dplyr_1.1.4             bookdown_0.41           BiocVersion_3.21.1     
## [40] fastmap_1.2.0           cli_3.6.3               magrittr_2.0.3         
## [43] utf8_1.2.4              filelock_1.0.3          UCSC.utils_1.3.0       
## [46] promises_1.3.0          rappdirs_0.3.3          bit64_4.5.2            
## [49] rmarkdown_2.29          XVector_0.47.0          httr_1.4.7             
## [52] bit_4.5.0               png_0.1-8               memoise_2.0.1          
## [55] evaluate_1.0.1          knitr_1.49              IRanges_2.41.0         
## [58] BiocFileCache_2.15.0    rlang_1.1.4             Rcpp_1.0.13-1          
## [61] xtable_1.8-4            glue_1.8.0              DBI_1.2.3              
## [64] BiocManager_1.30.25     BiocGenerics_0.53.1     jsonlite_1.8.9         
## [67] R6_2.5.1                zlibbioc_1.53.0