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 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-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_1.6.2 shiny_1.10.0        BiocStyle_2.34.0   
## 
## loaded via a namespace (and not attached):
##  [1] rappdirs_0.3.3          sass_0.4.9              generics_0.1.3         
##  [4] BiocVersion_3.20.0      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_3.14.0   
## [13] jsonlite_1.8.9          AnnotationDbi_1.68.0    GenomeInfoDb_1.42.3    
## [16] DBI_1.2.3               promises_1.3.2          BiocManager_1.30.25    
## [19] httr_1.4.7              UCSC.utils_1.2.0        Biostrings_2.74.1      
## [22] jquerylib_0.1.4         cli_3.6.3               crayon_1.5.3           
## [25] rlang_1.1.5             XVector_0.46.0          dbplyr_2.5.0           
## [28] Biobase_2.66.0          bit64_4.6.0-1           cachem_1.1.0           
## [31] yaml_2.3.10             tools_4.4.2             memoise_2.0.1          
## [34] dplyr_1.1.4             GenomeInfoDbData_1.2.13 filelock_1.0.3         
## [37] httpuv_1.6.15           ExperimentHub_2.14.0    BiocGenerics_0.52.0    
## [40] curl_6.2.0              png_0.1-8               vctrs_0.6.5            
## [43] R6_2.5.1                mime_0.12               stats4_4.4.2           
## [46] lifecycle_1.0.4         BiocFileCache_2.14.0    zlibbioc_1.52.0        
## [49] KEGGREST_1.46.0         IRanges_2.40.1          S4Vectors_0.44.0       
## [52] bit_4.5.0.1             pkgconfig_2.0.3         bslib_0.8.0            
## [55] pillar_1.10.1           later_1.4.1             glue_1.8.0             
## [58] Rcpp_1.0.14             xfun_0.50               tibble_3.2.1           
## [61] tidyselect_1.2.1        knitr_1.49              xtable_1.8-4           
## [64] htmltools_0.5.8.1       rmarkdown_2.29          compiler_4.4.2