epicompare 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 Under development (unstable) (2025-11-04 r88984)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.8
##
## Matrix products: default
## BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] EpiCompare_1.15.2 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.6.0
## [2] BiocIO_1.21.0
## [3] bitops_1.0-9
## [4] ggplotify_0.1.3
## [5] filelock_1.0.3
## [6] tibble_3.3.0
## [7] R.oo_1.27.1
## [8] polyclip_1.10-7
## [9] XML_3.99-0.20
## [10] lifecycle_1.0.4
## [11] httr2_1.2.2
## [12] lattice_0.22-7
## [13] MASS_7.3-65
## [14] magrittr_2.0.4
## [15] plotly_4.11.0
## [16] sass_0.4.10
## [17] rmarkdown_2.30
## [18] jquerylib_0.1.4
## [19] yaml_2.3.12
## [20] plotrix_3.8-13
## [21] otel_0.2.0
## [22] ggtangle_0.0.9
## [23] cowplot_1.2.0
## [24] DBI_1.2.3
## [25] RColorBrewer_1.1-3
## [26] lubridate_1.9.4
## [27] abind_1.4-8
## [28] GenomicRanges_1.63.1
## [29] purrr_1.2.0
## [30] R.utils_2.13.0
## [31] BiocGenerics_0.57.0
## [32] RCurl_1.98-1.17
## [33] yulab.utils_0.2.2
## [34] tweenr_2.0.3
## [35] rappdirs_0.3.3
## [36] gdtools_0.4.4
## [37] IRanges_2.45.0
## [38] S4Vectors_0.49.0
## [39] enrichplot_1.31.2
## [40] ggrepel_0.9.6
## [41] tidytree_0.4.6
## [42] ChIPseeker_1.47.1
## [43] codetools_0.2-20
## [44] DelayedArray_0.37.0
## [45] DOSE_4.5.0
## [46] ggforce_0.5.0
## [47] tidyselect_1.2.1
## [48] aplot_0.2.9
## [49] UCSC.utils_1.7.1
## [50] farver_2.1.2
## [51] base64enc_0.1-3
## [52] matrixStats_1.5.0
## [53] stats4_4.6.0
## [54] BiocFileCache_3.1.0
## [55] Seqinfo_1.1.0
## [56] GenomicAlignments_1.47.0
## [57] jsonlite_2.0.0
## [58] systemfonts_1.3.1
## [59] tools_4.6.0
## [60] ggnewscale_0.5.2
## [61] treeio_1.35.0
## [62] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
## [63] Rcpp_1.1.0.8.1
## [64] glue_1.8.0
## [65] SparseArray_1.11.8
## [66] xfun_0.54
## [67] qvalue_2.43.0
## [68] MatrixGenerics_1.23.0
## [69] GenomeInfoDb_1.47.2
## [70] dplyr_1.1.4
## [71] withr_3.0.2
## [72] BiocManager_1.30.27
## [73] fastmap_1.2.0
## [74] boot_1.3-32
## [75] caTools_1.18.3
## [76] digest_0.6.39
## [77] mime_0.13
## [78] timechange_0.3.0
## [79] R6_2.6.1
## [80] gridGraphics_0.5-1
## [81] seqPattern_1.43.0
## [82] GO.db_3.22.0
## [83] gtools_3.9.5
## [84] dichromat_2.0-0.1
## [85] RSQLite_2.4.5
## [86] cigarillo_1.1.0
## [87] R.methodsS3_1.8.2
## [88] tidyr_1.3.1
## [89] generics_0.1.4
## [90] fontLiberation_0.1.0
## [91] data.table_1.17.8
## [92] bsplus_0.1.5
## [93] rtracklayer_1.71.1
## [94] httr_1.4.7
## [95] htmlwidgets_1.6.4
## [96] S4Arrays_1.11.1
## [97] scatterpie_0.2.6
## [98] downloadthis_0.5.0
## [99] pkgconfig_2.0.3
## [100] gtable_0.3.6
## [101] blob_1.2.4
## [102] impute_1.85.0
## [103] S7_0.2.1
## [104] XVector_0.51.0
## [105] htmltools_0.5.9
## [106] fontBitstreamVera_0.1.1
## [107] bookdown_0.46
## [108] fgsea_1.37.2
## [109] scales_1.4.0
## [110] Biobase_2.71.0
## [111] png_0.1-8
## [112] ggfun_0.2.0
## [113] knitr_1.50
## [114] tzdb_0.5.0
## [115] reshape2_1.4.5
## [116] rjson_0.2.23
## [117] nlme_3.1-168
## [118] curl_7.0.0
## [119] cachem_1.1.0
## [120] stringr_1.6.0
## [121] BiocVersion_3.23.1
## [122] KernSmooth_2.23-26
## [123] parallel_4.6.0
## [124] AnnotationDbi_1.73.0
## [125] restfulr_0.0.16
## [126] pillar_1.11.1
## [127] grid_4.6.0
## [128] vctrs_0.6.5
## [129] gplots_3.3.0
## [130] tidydr_0.0.6
## [131] dbplyr_2.5.1
## [132] cluster_2.1.8.1
## [133] evaluate_1.0.5
## [134] magick_2.9.0
## [135] tinytex_0.58
## [136] readr_2.1.6
## [137] GenomicFeatures_1.63.1
## [138] cli_3.6.5
## [139] compiler_4.6.0
## [140] Rsamtools_2.27.0
## [141] rlang_1.1.6
## [142] crayon_1.5.3
## [143] labeling_0.4.3
## [144] plyr_1.8.9
## [145] fs_1.6.6
## [146] ggiraph_0.9.2
## [147] stringi_1.8.7
## [148] viridisLite_0.4.2
## [149] gridBase_0.4-7
## [150] genomation_1.43.0
## [151] BiocParallel_1.45.0
## [152] Biostrings_2.79.2
## [153] lazyeval_0.2.2
## [154] GOSemSim_2.37.0
## [155] fontquiver_0.2.1
## [156] Matrix_1.7-4
## [157] BSgenome_1.79.1
## [158] hms_1.1.4
## [159] patchwork_1.3.2
## [160] bit64_4.6.0-1
## [161] ggplot2_4.0.1
## [162] KEGGREST_1.51.1
## [163] SummarizedExperiment_1.41.0
## [164] AnnotationHub_4.1.0
## [165] igraph_2.2.1
## [166] memoise_2.0.1
## [167] bslib_0.9.0
## [168] ggtree_4.1.1
## [169] fastmatch_1.1-6
## [170] bit_4.6.0
## [171] ape_5.8-1