vignettes/docker.Rmd
docker.RmdKGExplorer is now available via ghcr.io as a containerised environment with Rstudio and all necessary dependencies pre-installed.
First, install Docker if you have not already.
Create an image of the Docker container in command line:
docker pull ghcr.io/neurogenomics/KGExplorerOnce the image has been created, you can launch it with:
docker run \
-d \
-e ROOT=true \
-e PASSWORD="<your_password>" \
-v ~/Desktop:/Desktop \
-v /Volumes:/Volumes \
-p 8900:8787 \
ghcr.io/neurogenomics/KGExplorer<your_password> above with
whatever you want your password to be.-v flags for your
particular use case.-d ensures the container will run in “detached”
mode, which means it will persist even after you’ve closed your command
line session.If you are using a system that does not allow Docker (as is the case for many institutional computing clusters), you can instead install Docker images via Singularity.
singularity pull docker://ghcr.io/neurogenomics/KGExplorerFor troubleshooting, see the Singularity documentation.
Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8900/
Login using the credentials set during the Installation steps.
utils::sessionInfo()## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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=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: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] KGExplorer_0.99.09
##
## loaded via a namespace (and not attached):
## [1] grr_0.9.5 httr2_1.2.1
## [3] rlang_1.1.6 magrittr_2.0.3
## [5] clue_0.3-66 GetoptLong_1.0.5
## [7] matrixStats_1.5.0 compiler_4.5.1
## [9] png_0.1-8 systemfonts_1.2.3
## [11] vctrs_0.6.5 maps_3.4.3
## [13] gprofiler2_0.2.3 stringr_1.5.1
## [15] rvest_1.0.4 shape_1.4.6.1
## [17] pkgconfig_2.0.3 crayon_1.5.3
## [19] fastmap_1.2.0 backports_1.5.0
## [21] promises_1.3.3 rmarkdown_2.29
## [23] ragg_1.4.0 purrr_1.1.0
## [25] xfun_0.52 cachem_1.1.0
## [27] pals_1.10 aplot_0.2.8
## [29] jsonlite_2.0.0 later_1.4.2
## [31] BiocParallel_1.43.4 cluster_2.1.8.1
## [33] broom_1.0.9 parallel_4.5.1
## [35] R6_2.6.1 rols_3.5.0
## [37] stringi_1.8.7 bslib_0.9.0
## [39] RColorBrewer_1.1-3 car_3.1-3
## [41] jquerylib_0.1.4 Rcpp_1.1.0
## [43] iterators_1.0.14 knitr_1.50
## [45] IRanges_2.43.0 httpuv_1.6.16
## [47] igraph_2.1.4 Matrix_1.7-3
## [49] tidyselect_1.2.1 dichromat_2.0-0.1
## [51] abind_1.4-8 yaml_2.3.10
## [53] doParallel_1.0.17 codetools_0.2-20
## [55] lattice_0.22-7 tibble_3.3.0
## [57] shiny_1.11.1 Biobase_2.69.0
## [59] treeio_1.33.0 evaluate_1.0.4
## [61] gridGraphics_0.5-1 desc_1.4.3
## [63] xml2_1.3.8 circlize_0.4.16
## [65] pillar_1.11.0 ggtree_3.17.1
## [67] ggpubr_0.6.1 carData_3.0-5
## [69] foreach_1.5.2 stats4_4.5.1
## [71] ggfun_0.2.0 plotly_4.11.0
## [73] generics_0.1.4 S4Vectors_0.47.0
## [75] ggplot2_3.5.2 scales_1.4.0
## [77] tidytree_0.4.6 xtable_1.8-4
## [79] glue_1.8.0 orthogene_1.15.0
## [81] mapproj_1.2.12 scatterplot3d_0.3-44
## [83] lazyeval_0.2.2 tools_4.5.1
## [85] data.table_1.17.8 ggsignif_0.6.4
## [87] babelgene_22.9 fs_1.6.6
## [89] tidygraph_1.3.1 fastmatch_1.1-6
## [91] grid_4.5.1 tidyr_1.3.1
## [93] ape_5.8-1 colorspace_2.1-1
## [95] nlme_3.1-168 patchwork_1.3.1
## [97] homologene_1.4.68.19.3.27 Formula_1.2-5
## [99] cli_3.6.5 rappdirs_0.3.3
## [101] Polychrome_1.5.4 textshaping_1.0.1
## [103] viridisLite_0.4.2 ComplexHeatmap_2.25.2
## [105] dplyr_1.1.4 gtable_0.3.6
## [107] rstatix_0.7.2 yulab.utils_0.2.0
## [109] sass_0.4.10 digest_0.6.37
## [111] BiocGenerics_0.55.1 ggplotify_0.1.2
## [113] rjson_0.2.23 htmlwidgets_1.6.4
## [115] farver_2.1.2 htmltools_0.5.8.1
## [117] pkgdown_2.1.3 simona_1.7.1
## [119] lifecycle_1.0.4 httr_1.4.7
## [121] mime_0.13 GlobalOptions_0.1.2