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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-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_1.2.0 shiny_1.7.5.1 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.42.0 xfun_0.40
## [3] bslib_0.5.1 Biobase_2.62.0
## [5] vctrs_0.6.4 tools_4.3.1
## [7] bitops_1.0-7 generics_0.1.3
## [9] stats4_4.3.1 curl_5.1.0
## [11] tibble_3.2.1 fansi_1.0.5
## [13] AnnotationDbi_1.64.0 RSQLite_2.3.1
## [15] blob_1.2.4 pkgconfig_2.0.3
## [17] dbplyr_2.3.4 S4Vectors_0.40.0
## [19] GenomeInfoDbData_1.2.11 lifecycle_1.0.3
## [21] compiler_4.3.1 Biostrings_2.70.0
## [23] httpuv_1.6.12 GenomeInfoDb_1.38.0
## [25] htmltools_0.5.6.1 sass_0.4.7
## [27] RCurl_1.98-1.12 yaml_2.3.7
## [29] interactiveDisplayBase_1.40.0 later_1.3.1
## [31] pillar_1.9.0 crayon_1.5.2
## [33] jquerylib_0.1.4 ellipsis_0.3.2
## [35] cachem_1.0.8 mime_0.12
## [37] ExperimentHub_2.10.0 AnnotationHub_3.10.0
## [39] tidyselect_1.2.0 digest_0.6.33
## [41] dplyr_1.1.3 bookdown_0.36
## [43] BiocVersion_3.18.0 fastmap_1.1.1
## [45] cli_3.6.1 magrittr_2.0.3
## [47] utf8_1.2.4 filelock_1.0.2
## [49] promises_1.2.1 rappdirs_0.3.3
## [51] bit64_4.0.5 rmarkdown_2.25
## [53] XVector_0.42.0 httr_1.4.7
## [55] bit_4.0.5 png_0.1-8
## [57] memoise_2.0.1 evaluate_0.22
## [59] knitr_1.44 IRanges_2.36.0
## [61] BiocFileCache_2.10.0 rlang_1.1.1
## [63] Rcpp_1.0.11 xtable_1.8-4
## [65] glue_1.6.2 DBI_1.1.3
## [67] BiocManager_1.30.22 BiocGenerics_0.48.0
## [69] jsonlite_1.8.7 R6_2.5.1
## [71] zlibbioc_1.48.0