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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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_1.3.1 shiny_1.8.1.1       BiocStyle_2.31.0   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.43.0         xfun_0.43               bslib_0.7.0            
##  [4] Biobase_2.63.1          vctrs_0.6.5             tools_4.4.0            
##  [7] generics_0.1.3          stats4_4.4.0            curl_5.2.1             
## [10] tibble_3.2.1            fansi_1.0.6             AnnotationDbi_1.65.2   
## [13] RSQLite_2.3.6           highr_0.10              blob_1.2.4             
## [16] pkgconfig_2.0.3         dbplyr_2.5.0            S4Vectors_0.41.7       
## [19] lifecycle_1.0.4         GenomeInfoDbData_1.2.12 compiler_4.4.0         
## [22] Biostrings_2.71.6       httpuv_1.6.15           GenomeInfoDb_1.39.14   
## [25] htmltools_0.5.8.1       sass_0.4.9              yaml_2.3.8             
## [28] later_1.3.2             pillar_1.9.0            crayon_1.5.2           
## [31] jquerylib_0.1.4         cachem_1.0.8            mime_0.12              
## [34] ExperimentHub_2.11.3    AnnotationHub_3.11.5    tidyselect_1.2.1       
## [37] digest_0.6.35           dplyr_1.1.4             bookdown_0.39          
## [40] BiocVersion_3.19.1      fastmap_1.1.1           cli_3.6.2              
## [43] magrittr_2.0.3          utf8_1.2.4              filelock_1.0.3         
## [46] UCSC.utils_0.99.7       promises_1.3.0          rappdirs_0.3.3         
## [49] bit64_4.0.5             rmarkdown_2.26          XVector_0.43.1         
## [52] httr_1.4.7              bit_4.0.5               png_0.1-8              
## [55] memoise_2.0.1           evaluate_0.23           knitr_1.46             
## [58] IRanges_2.37.1          BiocFileCache_2.11.2    rlang_1.1.3            
## [61] Rcpp_1.0.12             xtable_1.8-4            glue_1.7.0             
## [64] DBI_1.2.2               BiocManager_1.30.22     BiocGenerics_0.49.1    
## [67] jsonlite_1.8.8          R6_2.5.1                zlibbioc_1.49.3