vignettes/docker.Rmd
docker.RmdMSTExplorer 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/MSTExplorerOnce 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/MSTExplorer<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/MSTExplorerFor 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 Under development (unstable) (2025-11-30 r89082)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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] MSTExplorer_1.0.10
##
## loaded via a namespace (and not attached):
## [1] later_1.4.4 bitops_1.0-9
## [3] ggplotify_0.1.3 GeneOverlap_1.47.0
## [5] filelock_1.0.3 tibble_3.3.0
## [7] lifecycle_1.0.4 httr2_1.2.1
## [9] KGExplorer_0.99.10 rstatix_0.7.3
## [11] HPOExplorer_1.0.6 doParallel_1.0.17
## [13] lattice_0.22-7 pals_1.10
## [15] backports_1.5.0 magrittr_2.0.4
## [17] limma_3.67.0 plotly_4.11.0
## [19] sass_0.4.10 rmarkdown_2.30
## [21] jquerylib_0.1.4 yaml_2.3.11
## [23] httpuv_1.6.16 otel_0.2.0
## [25] HGNChelper_0.8.15 mapproj_1.2.12
## [27] DBI_1.2.3 RColorBrewer_1.1-3
## [29] maps_3.4.3 abind_1.4-8
## [31] GenomicRanges_1.63.0 rvest_1.0.5
## [33] purrr_1.2.0 BiocGenerics_0.57.0
## [35] yulab.utils_0.2.2 rappdirs_0.3.3
## [37] gdtools_0.4.4 circlize_0.4.16
## [39] IRanges_2.45.0 S4Vectors_0.49.0
## [41] rols_2.99.5 tidytree_0.4.6
## [43] piggyback_0.1.5 pkgdown_2.2.0
## [45] DelayedArray_0.37.0 codetools_0.2-20
## [47] xml2_1.5.1 tidyselect_1.2.1
## [49] shape_1.4.6.1 aplot_0.2.9
## [51] farver_2.1.2 matrixStats_1.5.0
## [53] stats4_4.6.0 BiocFileCache_3.1.0
## [55] Seqinfo_1.1.0 jsonlite_2.0.0
## [57] GetoptLong_1.1.0 tidygraph_1.3.1
## [59] Formula_1.2-5 iterators_1.0.14
## [61] systemfonts_1.3.1 foreach_1.5.2
## [63] tools_4.6.0 treeio_1.35.0
## [65] ragg_1.5.0 Rcpp_1.1.0
## [67] glue_1.8.0 SparseArray_1.11.6
## [69] xfun_0.54 MatrixGenerics_1.23.0
## [71] RNOmni_1.0.1.2 dplyr_1.1.4
## [73] BiocManager_1.30.27 fastmap_1.2.0
## [75] caTools_1.18.3 digest_0.6.39
## [77] R6_2.6.1 mime_0.13
## [79] gridGraphics_0.5-1 textshaping_1.0.4
## [81] colorspace_2.1-2 gtools_3.9.5
## [83] dichromat_2.0-0.1 RSQLite_2.4.5
## [85] tidyr_1.3.1 generics_0.1.4
## [87] fontLiberation_0.1.0 data.table_1.17.8
## [89] S4Arrays_1.11.1 httr_1.4.7
## [91] htmlwidgets_1.6.4 scatterplot3d_0.3-44
## [93] pkgconfig_2.0.3 gtable_0.3.6
## [95] blob_1.2.4 ComplexHeatmap_2.27.0
## [97] S7_0.2.1 SingleCellExperiment_1.33.0
## [99] XVector_0.51.0 htmltools_0.5.8.1
## [101] fontBitstreamVera_0.1.1 carData_3.0-5
## [103] clue_0.3-66 scales_1.4.0
## [105] Biobase_2.71.0 png_0.1-8
## [107] ggfun_0.2.0 knitr_1.50
## [109] reshape2_1.4.5 rjson_0.2.23
## [111] nlme_3.1-168 curl_7.0.0
## [113] cachem_1.1.0 GlobalOptions_0.1.3
## [115] Polychrome_1.5.4 stringr_1.6.0
## [117] BiocVersion_3.23.1 KernSmooth_2.23-26
## [119] parallel_4.6.0 AnnotationDbi_1.73.0
## [121] desc_1.4.3 pillar_1.11.1
## [123] grid_4.6.0 vctrs_0.6.5
## [125] gplots_3.3.0 promises_1.5.0
## [127] ggpubr_0.6.2 car_3.1-3
## [129] dbplyr_2.5.1 xtable_1.8-4
## [131] cluster_2.1.8.1 evaluate_1.0.5
## [133] orthogene_1.17.0 cli_3.6.5
## [135] compiler_4.6.0 rlang_1.1.6
## [137] crayon_1.5.3 grr_0.9.5
## [139] simona_1.9.0 ggsignif_0.6.4
## [141] gprofiler2_0.2.4 plyr_1.8.9
## [143] EWCE_1.19.0 fs_1.6.6
## [145] ggiraph_0.9.2 stringi_1.8.7
## [147] viridisLite_0.4.2 ewceData_1.19.0
## [149] BiocParallel_1.45.0 babelgene_22.9
## [151] Biostrings_2.79.2 lazyeval_0.2.2
## [153] homologene_1.4.68.19.3.27 fontquiver_0.2.1
## [155] Matrix_1.7-4 ExperimentHub_3.1.0
## [157] patchwork_1.3.2 bit64_4.6.0-1
## [159] ggplot2_4.0.1 statmod_1.5.1
## [161] KEGGREST_1.51.1 shiny_1.11.1
## [163] SummarizedExperiment_1.41.0 AnnotationHub_4.1.0
## [165] igraph_2.2.1 broom_1.0.10
## [167] memoise_2.0.1 bslib_0.9.0
## [169] ggtree_4.1.1 fastmatch_1.1-6
## [171] bit_4.6.0 splitstackshape_1.4.8
## [173] ape_5.8-1