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 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.6.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## 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_1.2.0 shiny_1.7.4.1       BiocStyle_2.30.0   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.42.0               xfun_0.39                    
##  [3] bslib_0.5.0                   Biobase_2.62.0               
##  [5] vctrs_0.6.3                   tools_4.3.1                  
##  [7] bitops_1.0-7                  generics_0.1.3               
##  [9] stats4_4.3.1                  curl_5.0.1                   
## [11] tibble_3.2.1                  fansi_1.0.4                  
## [13] AnnotationDbi_1.64.0          RSQLite_2.3.1                
## [15] highr_0.10                    blob_1.2.4                   
## [17] pkgconfig_2.0.3               dbplyr_2.3.3                 
## [19] S4Vectors_0.40.1              GenomeInfoDbData_1.2.10      
## [21] lifecycle_1.0.3               compiler_4.3.1               
## [23] Biostrings_2.70.1             httpuv_1.6.11                
## [25] GenomeInfoDb_1.38.0           htmltools_0.5.5              
## [27] sass_0.4.6                    RCurl_1.98-1.12              
## [29] yaml_2.3.7                    interactiveDisplayBase_1.40.0
## [31] later_1.3.1                   pillar_1.9.0                 
## [33] crayon_1.5.2                  jquerylib_0.1.4              
## [35] ellipsis_0.3.2                cachem_1.0.8                 
## [37] mime_0.12                     ExperimentHub_2.10.0         
## [39] AnnotationHub_3.10.0          tidyselect_1.2.0             
## [41] digest_0.6.33                 dplyr_1.1.2                  
## [43] bookdown_0.34                 BiocVersion_3.18.0           
## [45] fastmap_1.1.1                 cli_3.6.1                    
## [47] magrittr_2.0.3                utf8_1.2.3                   
## [49] filelock_1.0.2                promises_1.2.0.1             
## [51] rappdirs_0.3.3                bit64_4.0.5                  
## [53] rmarkdown_2.23                XVector_0.42.0               
## [55] httr_1.4.6                    bit_4.0.5                    
## [57] png_0.1-8                     memoise_2.0.1                
## [59] evaluate_0.21                 knitr_1.43                   
## [61] IRanges_2.36.0                BiocFileCache_2.10.1         
## [63] rlang_1.1.1                   Rcpp_1.0.11                  
## [65] xtable_1.8-4                  glue_1.6.2                   
## [67] DBI_1.1.3                     BiocManager_1.30.22          
## [69] BiocGenerics_0.48.0           jsonlite_1.8.7               
## [71] R6_2.5.1                      zlibbioc_1.48.0