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 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] MSTExplorer_1.0.9
##
## loaded via a namespace (and not attached):
## [1] later_1.4.2 bitops_1.0-9
## [3] ggplotify_0.1.2 GeneOverlap_1.45.0
## [5] filelock_1.0.3 tibble_3.3.0
## [7] lifecycle_1.0.4 httr2_1.2.1
## [9] KGExplorer_0.99.09 rstatix_0.7.2
## [11] HPOExplorer_1.0.5 doParallel_1.0.17
## [13] lattice_0.22-7 pals_1.10
## [15] backports_1.5.0 magrittr_2.0.3
## [17] limma_3.65.3 plotly_4.11.0
## [19] sass_0.4.10 rmarkdown_2.29
## [21] jquerylib_0.1.4 yaml_2.3.10
## [23] httpuv_1.6.16 HGNChelper_0.8.15
## [25] mapproj_1.2.12 DBI_1.2.3
## [27] RColorBrewer_1.1-3 maps_3.4.3
## [29] abind_1.4-8 GenomicRanges_1.61.1
## [31] rvest_1.0.4 purrr_1.1.0
## [33] BiocGenerics_0.55.1 yulab.utils_0.2.0
## [35] rappdirs_0.3.3 circlize_0.4.16
## [37] IRanges_2.43.0 S4Vectors_0.47.0
## [39] rols_3.5.0 tidytree_0.4.6
## [41] piggyback_0.1.5 pkgdown_2.1.3
## [43] codetools_0.2-20 DelayedArray_0.35.2
## [45] xml2_1.3.8 tidyselect_1.2.1
## [47] shape_1.4.6.1 aplot_0.2.8
## [49] farver_2.1.2 matrixStats_1.5.0
## [51] stats4_4.5.1 BiocFileCache_2.99.5
## [53] Seqinfo_0.99.2 jsonlite_2.0.0
## [55] GetoptLong_1.0.5 tidygraph_1.3.1
## [57] Formula_1.2-5 iterators_1.0.14
## [59] systemfonts_1.2.3 foreach_1.5.2
## [61] tools_4.5.1 treeio_1.33.0
## [63] ragg_1.4.0 Rcpp_1.1.0
## [65] glue_1.8.0 SparseArray_1.9.1
## [67] xfun_0.52 MatrixGenerics_1.21.0
## [69] RNOmni_1.0.1.2 dplyr_1.1.4
## [71] BiocManager_1.30.26 fastmap_1.2.0
## [73] caTools_1.18.3 digest_0.6.37
## [75] R6_2.6.1 mime_0.13
## [77] gridGraphics_0.5-1 textshaping_1.0.1
## [79] colorspace_2.1-1 gtools_3.9.5
## [81] dichromat_2.0-0.1 RSQLite_2.4.2
## [83] tidyr_1.3.1 generics_0.1.4
## [85] data.table_1.17.8 httr_1.4.7
## [87] htmlwidgets_1.6.4 S4Arrays_1.9.1
## [89] scatterplot3d_0.3-44 pkgconfig_2.0.3
## [91] gtable_0.3.6 blob_1.2.4
## [93] ComplexHeatmap_2.25.2 SingleCellExperiment_1.31.1
## [95] XVector_0.49.0 htmltools_0.5.8.1
## [97] carData_3.0-5 clue_0.3-66
## [99] scales_1.4.0 Biobase_2.69.0
## [101] png_0.1-8 ggfun_0.2.0
## [103] knitr_1.50 reshape2_1.4.4
## [105] rjson_0.2.23 nlme_3.1-168
## [107] curl_6.4.0 cachem_1.1.0
## [109] GlobalOptions_0.1.2 Polychrome_1.5.4
## [111] stringr_1.5.1 BiocVersion_3.22.0
## [113] KernSmooth_2.23-26 parallel_4.5.1
## [115] AnnotationDbi_1.71.1 desc_1.4.3
## [117] pillar_1.11.0 grid_4.5.1
## [119] vctrs_0.6.5 gplots_3.2.0
## [121] promises_1.3.3 ggpubr_0.6.1
## [123] car_3.1-3 dbplyr_2.5.0
## [125] xtable_1.8-4 cluster_2.1.8.1
## [127] evaluate_1.0.4 orthogene_1.15.0
## [129] cli_3.6.5 compiler_4.5.1
## [131] rlang_1.1.6 crayon_1.5.3
## [133] grr_0.9.5 simona_1.7.1
## [135] ggsignif_0.6.4 gprofiler2_0.2.3
## [137] plyr_1.8.9 EWCE_1.15.1
## [139] fs_1.6.6 stringi_1.8.7
## [141] viridisLite_0.4.2 ewceData_1.17.0
## [143] BiocParallel_1.43.4 babelgene_22.9
## [145] Biostrings_2.77.2 lazyeval_0.2.2
## [147] homologene_1.4.68.19.3.27 Matrix_1.7-3
## [149] ExperimentHub_2.99.5 patchwork_1.3.1
## [151] bit64_4.6.0-1 ggplot2_3.5.2
## [153] statmod_1.5.0 KEGGREST_1.49.1
## [155] shiny_1.11.1 SummarizedExperiment_1.39.1
## [157] AnnotationHub_3.99.6 igraph_2.1.4
## [159] broom_1.0.9 memoise_2.0.1
## [161] bslib_0.9.0 ggtree_3.17.1
## [163] fastmatch_1.1-6 bit_4.6.0
## [165] splitstackshape_1.4.8 ape_5.8-1