Bioconductor Code: BiocHubsShiny (original) (raw)

# 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 ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocHubsShiny") ``` # Loading the package ``` r library(BiocHubsShiny) ``` # Display of resources Resources are displayed interactively using the eponymous function: ``` r 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 ``` r sessionInfo() #> R Under development (unstable) (2025-04-02 r88102) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 #> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 LAPACK version 3.10.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [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_1.7.5 shiny_1.10.0 colorout_1.2-2 #> #> loaded via a namespace (and not attached): #> [1] rappdirs_0.3.3 generics_0.1.3 BiocVersion_3.21.1 #> [4] RSQLite_2.3.9 digest_0.6.37 magrittr_2.0.3 #> [7] evaluate_1.0.3 fastmap_1.2.0 blob_1.2.4 #> [10] jsonlite_2.0.0 AnnotationHub_3.15.1 AnnotationDbi_1.69.0 #> [13] GenomeInfoDb_1.43.4 DBI_1.2.3 promises_1.3.2 #> [16] BiocManager_1.30.25 httr_1.4.7 UCSC.utils_1.3.1 #> [19] Biostrings_2.75.4 codetools_0.2-20 httr2_1.1.2 #> [22] cli_3.6.4 crayon_1.5.3 rlang_1.1.5 #> [25] XVector_0.47.2 dbplyr_2.5.0 Biobase_2.67.0 #> [28] bit64_4.6.0-1 cachem_1.1.0 yaml_2.3.10 #> [31] tools_4.6.0 memoise_2.0.1 dplyr_1.1.4 #> [34] GenomeInfoDbData_1.2.14 httpuv_1.6.15 filelock_1.0.3 #> [37] ExperimentHub_2.15.1 BiocGenerics_0.53.6 curl_6.2.2 #> [40] png_0.1-8 vctrs_0.6.5 R6_2.6.1 #> [43] mime_0.13 stats4_4.6.0 BiocFileCache_2.15.1 #> [46] lifecycle_1.0.4 KEGGREST_1.47.1 IRanges_2.41.3 #> [49] S4Vectors_0.45.4 bit_4.6.0 pkgconfig_2.0.3 #> [52] pillar_1.10.1 later_1.4.1 glue_1.8.0 #> [55] Rcpp_1.0.14 xfun_0.52 tibble_3.2.1 #> [58] tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.50 #> [61] xtable_1.8-4 htmltools_0.5.8.1 rmarkdown_2.29 #> [64] compiler_4.6.0 ```