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 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-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_1.0.0 shiny_1.7.4 BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.40.0 xfun_0.39
## [3] bslib_0.4.2 Biobase_2.60.0
## [5] vctrs_0.6.2 tools_4.3.0
## [7] bitops_1.0-7 generics_0.1.3
## [9] stats4_4.3.0 curl_5.0.0
## [11] tibble_3.2.1 fansi_1.0.4
## [13] AnnotationDbi_1.62.0 RSQLite_2.3.1
## [15] highr_0.10 blob_1.2.4
## [17] pkgconfig_2.0.3 dbplyr_2.3.2
## [19] S4Vectors_0.38.0 GenomeInfoDbData_1.2.10
## [21] lifecycle_1.0.3 compiler_4.3.0
## [23] Biostrings_2.68.0 httpuv_1.6.9
## [25] GenomeInfoDb_1.36.0 htmltools_0.5.5
## [27] sass_0.4.5 RCurl_1.98-1.12
## [29] yaml_2.3.7 interactiveDisplayBase_1.38.0
## [31] later_1.3.0 pillar_1.9.0
## [33] crayon_1.5.2 jquerylib_0.1.4
## [35] ellipsis_0.3.2 cachem_1.0.7
## [37] mime_0.12 ExperimentHub_2.8.0
## [39] AnnotationHub_3.8.0 tidyselect_1.2.0
## [41] digest_0.6.31 dplyr_1.1.2
## [43] bookdown_0.33 BiocVersion_3.17.1
## [45] fastmap_1.1.1 cli_3.6.1
## [47] magrittr_2.0.3 utf8_1.2.3
## [49] filelock_1.0.2 promises_1.2.0.1
## [51] rappdirs_0.3.3 bit64_4.0.5
## [53] rmarkdown_2.21 XVector_0.40.0
## [55] httr_1.4.5 bit_4.0.5
## [57] png_0.1-8 memoise_2.0.1
## [59] evaluate_0.20 knitr_1.42
## [61] IRanges_2.34.0 BiocFileCache_2.8.0
## [63] rlang_1.1.0 Rcpp_1.0.10
## [65] xtable_1.8-4 glue_1.6.2
## [67] DBI_1.1.3 BiocManager_1.30.20
## [69] BiocGenerics_0.46.0 jsonlite_1.8.4
## [71] R6_2.5.1 zlibbioc_1.46.0