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.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocHubsShiny")

Loading the package

library(BiocHubsShiny)

Display of resources

Resources are displayed interactively using the eponymous function:

BiocHubsShiny()

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:

Selection

Click on the rows to select the resources. They will show up as highlighted rows.

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.

Session Info

sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        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: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocHubsShiny_1.5.1 shiny_1.9.1         BiocStyle_2.33.1   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.45.1         xfun_0.47               bslib_0.8.0            
##  [4] Biobase_2.65.0          vctrs_0.6.5             tools_4.4.1            
##  [7] generics_0.1.3          stats4_4.4.1            curl_5.2.1             
## [10] tibble_3.2.1            fansi_1.0.6             AnnotationDbi_1.67.0   
## [13] RSQLite_2.3.7           highr_0.11              blob_1.2.4             
## [16] pkgconfig_2.0.3         dbplyr_2.5.0            S4Vectors_0.43.2       
## [19] GenomeInfoDbData_1.2.12 lifecycle_1.0.4         compiler_4.4.1         
## [22] Biostrings_2.73.1       httpuv_1.6.15           GenomeInfoDb_1.41.1    
## [25] htmltools_0.5.8.1       sys_3.4.2               buildtools_1.0.0       
## [28] sass_0.4.9              yaml_2.3.10             later_1.3.2            
## [31] pillar_1.9.0            crayon_1.5.3            jquerylib_0.1.4        
## [34] cachem_1.1.0            mime_0.12               ExperimentHub_2.13.1   
## [37] AnnotationHub_3.13.3    tidyselect_1.2.1        digest_0.6.37          
## [40] dplyr_1.1.4             BiocVersion_3.20.0      maketools_1.3.0        
## [43] fastmap_1.2.0           cli_3.6.3               magrittr_2.0.3         
## [46] utf8_1.2.4              filelock_1.0.3          UCSC.utils_1.1.0       
## [49] promises_1.3.0          rappdirs_0.3.3          bit64_4.0.5            
## [52] rmarkdown_2.28          XVector_0.45.0          httr_1.4.7             
## [55] bit_4.0.5               png_0.1-8               memoise_2.0.1          
## [58] evaluate_0.24.0         knitr_1.48              IRanges_2.39.2         
## [61] BiocFileCache_2.13.0    rlang_1.1.4             Rcpp_1.0.13            
## [64] xtable_1.8-4            glue_1.7.0              DBI_1.2.3              
## [67] BiocManager_1.30.24     BiocGenerics_0.51.0     jsonlite_1.8.8         
## [70] R6_2.5.1                zlibbioc_1.51.1