vignettes/docker.Rmd
docker.Rmdepicompare is now available via DockerHub 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 neurogenomicslab/epicompareOnce 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 8787:8787 \
neurogenomicslab/epicompare<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://neurogenomicslab/epicompareFinally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/
Login using the credentials set during the Installation steps.
utils::sessionInfo()## R version 4.6.0 (2026-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 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] EpiCompare_1.16.0 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] BiocIO_1.23.3
## [2] bitops_1.0-9
## [3] ggplotify_0.1.3
## [4] filelock_1.0.3
## [5] tibble_3.3.1
## [6] polyclip_1.10-7
## [7] enrichit_0.1.4
## [8] XML_3.99-0.23
## [9] lifecycle_1.0.5
## [10] httr2_1.2.2
## [11] lattice_0.22-9
## [12] MASS_7.3-65
## [13] magrittr_2.0.5
## [14] plotly_4.12.0
## [15] sass_0.4.10
## [16] rmarkdown_2.31
## [17] jquerylib_0.1.4
## [18] yaml_2.3.12
## [19] plotrix_3.8-14
## [20] otel_0.2.0
## [21] ggtangle_0.1.2
## [22] DBI_1.3.0
## [23] RColorBrewer_1.1-3
## [24] abind_1.4-8
## [25] GenomicRanges_1.65.0
## [26] purrr_1.2.2
## [27] BiocGenerics_0.59.0
## [28] RCurl_1.98-1.18
## [29] yulab.utils_0.2.4
## [30] tweenr_2.0.3
## [31] rappdirs_0.3.4
## [32] gdtools_0.5.0
## [33] IRanges_2.47.0
## [34] S4Vectors_0.51.1
## [35] enrichplot_1.33.0
## [36] ggrepel_0.9.8
## [37] tidytree_0.4.7
## [38] pkgdown_2.2.0
## [39] ChIPseeker_1.49.0
## [40] codetools_0.2-20
## [41] DelayedArray_0.39.1
## [42] DOSE_4.7.0
## [43] ggforce_0.5.0
## [44] tidyselect_1.2.1
## [45] aplot_0.2.9
## [46] UCSC.utils_1.9.0
## [47] farver_2.1.2
## [48] matrixStats_1.5.0
## [49] stats4_4.6.0
## [50] BiocFileCache_3.3.0
## [51] Seqinfo_1.3.0
## [52] GenomicAlignments_1.49.0
## [53] jsonlite_2.0.0
## [54] systemfonts_1.3.2
## [55] tools_4.6.0
## [56] ggnewscale_0.5.2
## [57] treeio_1.37.0
## [58] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
## [59] ragg_1.5.2
## [60] Rcpp_1.1.1-1.1
## [61] glue_1.8.1
## [62] SparseArray_1.13.2
## [63] BiocBaseUtils_1.15.0
## [64] xfun_0.57
## [65] MatrixGenerics_1.25.0
## [66] GenomeInfoDb_1.49.0
## [67] dplyr_1.2.1
## [68] withr_3.0.2
## [69] BiocManager_1.30.27
## [70] fastmap_1.2.0
## [71] boot_1.3-32
## [72] caTools_1.18.3
## [73] digest_0.6.39
## [74] R6_2.6.1
## [75] gridGraphics_0.5-1
## [76] seqPattern_1.45.0
## [77] textshaping_1.0.5
## [78] GO.db_3.23.1
## [79] gtools_3.9.5
## [80] RSQLite_3.52.0
## [81] cigarillo_1.3.0
## [82] tidyr_1.3.2
## [83] generics_0.1.4
## [84] fontLiberation_0.1.0
## [85] data.table_1.18.4
## [86] rtracklayer_1.73.0
## [87] httr_1.4.8
## [88] htmlwidgets_1.6.4
## [89] S4Arrays_1.13.0
## [90] scatterpie_0.2.6
## [91] downloadthis_0.5.0
## [92] pkgconfig_2.0.3
## [93] gtable_0.3.6
## [94] blob_1.3.0
## [95] S7_0.2.2
## [96] impute_1.87.0
## [97] XVector_0.53.0
## [98] htmltools_0.5.9
## [99] fontBitstreamVera_0.1.1
## [100] bookdown_0.46
## [101] scales_1.4.0
## [102] Biobase_2.73.1
## [103] png_0.1-9
## [104] ggfun_0.2.0
## [105] knitr_1.51
## [106] tzdb_0.5.0
## [107] reshape2_1.4.5
## [108] rjson_0.2.23
## [109] nlme_3.1-169
## [110] curl_7.1.0
## [111] cachem_1.1.0
## [112] stringr_1.6.0
## [113] BiocVersion_3.24.0
## [114] KernSmooth_2.23-26
## [115] parallel_4.6.0
## [116] AnnotationDbi_1.75.0
## [117] restfulr_0.0.16
## [118] desc_1.4.3
## [119] pillar_1.11.1
## [120] grid_4.6.0
## [121] vctrs_0.7.3
## [122] gplots_3.3.0
## [123] tidydr_0.0.6
## [124] dbplyr_2.5.2
## [125] cluster_2.1.8.2
## [126] evaluate_1.0.5
## [127] readr_2.2.0
## [128] GenomicFeatures_1.65.0
## [129] cli_3.6.6
## [130] compiler_4.6.0
## [131] Rsamtools_2.29.0
## [132] rlang_1.2.0
## [133] crayon_1.5.3
## [134] plyr_1.8.9
## [135] fs_2.1.0
## [136] ggiraph_0.9.6
## [137] stringi_1.8.7
## [138] viridisLite_0.4.3
## [139] genomation_1.45.0
## [140] gridBase_0.4-7
## [141] BiocParallel_1.47.0
## [142] Biostrings_2.81.1
## [143] lazyeval_0.2.3
## [144] GOSemSim_2.39.0
## [145] fontquiver_0.2.1
## [146] Matrix_1.7-5
## [147] BSgenome_1.81.0
## [148] hms_1.1.4
## [149] patchwork_1.3.2
## [150] bit64_4.8.0
## [151] ggplot2_4.0.3
## [152] KEGGREST_1.53.0
## [153] SummarizedExperiment_1.43.0
## [154] AnnotationHub_4.1.0
## [155] igraph_2.3.1
## [156] memoise_2.0.1
## [157] bslib_0.10.0
## [158] ggtree_4.3.0
## [159] bit_4.6.0
## [160] ape_5.8-1