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.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocHubsShiny")
Resources are displayed interactively using the eponymous function:
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:
Click on the rows to select the resources. They will show up as highlighted rows.
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.
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
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