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.
## R version 4.5.2 (2025-10-31)
## 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=C
## [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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] EpiCompare_1.14.0 BiocStyle_2.38.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.5.2
## [2] BiocIO_1.20.0
## [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] XML_3.99-0.20
## [9] lifecycle_1.0.4
## [10] httr2_1.2.1
## [11] lattice_0.22-7
## [12] magrittr_2.0.4
## [13] plotly_4.11.0
## [14] sass_0.4.10
## [15] rmarkdown_2.30
## [16] jquerylib_0.1.4
## [17] yaml_2.3.10
## [18] plotrix_3.8-4
## [19] ggtangle_0.0.8
## [20] cowplot_1.2.0
## [21] DBI_1.2.3
## [22] buildtools_1.0.0
## [23] RColorBrewer_1.1-3
## [24] lubridate_1.9.4
## [25] abind_1.4-8
## [26] GenomicRanges_1.63.0
## [27] purrr_1.2.0
## [28] R.utils_2.13.0
## [29] BiocGenerics_0.56.0
## [30] RCurl_1.98-1.17
## [31] yulab.utils_0.2.1
## [32] rappdirs_0.3.3
## [33] gdtools_0.4.4
## [34] IRanges_2.45.0
## [35] S4Vectors_0.49.0
## [36] enrichplot_1.31.0
## [37] ggrepel_0.9.6
## [38] tidytree_0.4.6
## [39] maketools_1.3.2
## [40] ChIPseeker_1.47.1
## [41] codetools_0.2-20
## [42] DelayedArray_0.37.0
## [43] DOSE_4.5.0
## [44] tidyselect_1.2.1
## [45] aplot_0.2.9
## [46] UCSC.utils_1.7.0
## [47] farver_2.1.2
## [48] matrixStats_1.5.0
## [49] stats4_4.5.2
## [50] BiocFileCache_3.0.0
## [51] base64enc_0.1-3
## [52] Seqinfo_1.1.0
## [53] GenomicAlignments_1.47.0
## [54] jsonlite_2.0.0
## [55] systemfonts_1.3.1
## [56] tools_4.5.2
## [57] treeio_1.35.0
## [58] TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1
## [59] Rcpp_1.1.0
## [60] glue_1.8.0
## [61] SparseArray_1.11.1
## [62] xfun_0.54
## [63] qvalue_2.43.0
## [64] MatrixGenerics_1.23.0
## [65] GenomeInfoDb_1.47.0
## [66] dplyr_1.1.4
## [67] withr_3.0.2
## [68] BiocManager_1.30.26
## [69] fastmap_1.2.0
## [70] boot_1.3-32
## [71] caTools_1.18.3
## [72] digest_0.6.37
## [73] timechange_0.3.0
## [74] R6_2.6.1
## [75] mime_0.13
## [76] gridGraphics_0.5-1
## [77] seqPattern_1.43.0
## [78] GO.db_3.22.0
## [79] gtools_3.9.5
## [80] RSQLite_2.4.4
## [81] cigarillo_1.1.0
## [82] R.methodsS3_1.8.2
## [83] tidyr_1.3.1
## [84] generics_0.1.4
## [85] fontLiberation_0.1.0
## [86] data.table_1.17.8
## [87] rtracklayer_1.69.1
## [88] bsplus_0.1.5
## [89] httr_1.4.7
## [90] htmlwidgets_1.6.4
## [91] S4Arrays_1.11.0
## [92] downloadthis_0.5.0
## [93] pkgconfig_2.0.3
## [94] gtable_0.3.6
## [95] blob_1.2.4
## [96] S7_0.2.0
## [97] impute_1.85.0
## [98] XVector_0.51.0
## [99] sys_3.4.3
## [100] htmltools_0.5.8.1
## [101] fontBitstreamVera_0.1.1
## [102] fgsea_1.37.0
## [103] scales_1.4.0
## [104] Biobase_2.70.0
## [105] png_0.1-8
## [106] ggfun_0.2.0
## [107] knitr_1.50
## [108] tzdb_0.5.0
## [109] reshape2_1.4.4
## [110] rjson_0.2.23
## [111] nlme_3.1-168
## [112] curl_7.0.0
## [113] cachem_1.1.0
## [114] stringr_1.6.0
## [115] BiocVersion_3.23.1
## [116] KernSmooth_2.23-26
## [117] parallel_4.5.2
## [118] AnnotationDbi_1.72.0
## [119] restfulr_0.0.16
## [120] pillar_1.11.1
## [121] grid_4.5.2
## [122] vctrs_0.6.5
## [123] gplots_3.2.0
## [124] dbplyr_2.5.1
## [125] evaluate_1.0.5
## [126] readr_2.1.5
## [127] GenomicFeatures_1.63.1
## [128] cli_3.6.5
## [129] compiler_4.5.2
## [130] Rsamtools_2.27.0
## [131] rlang_1.1.6
## [132] crayon_1.5.3
## [133] labeling_0.4.3
## [134] plyr_1.8.9
## [135] fs_1.6.6
## [136] ggiraph_0.9.2
## [137] stringi_1.8.7
## [138] genomation_1.41.1
## [139] viridisLite_0.4.2
## [140] gridBase_0.4-7
## [141] BiocParallel_1.44.0
## [142] Biostrings_2.78.0
## [143] lazyeval_0.2.2
## [144] GOSemSim_2.37.0
## [145] fontquiver_0.2.1
## [146] Matrix_1.7-4
## [147] BSgenome_1.79.1
## [148] hms_1.1.4
## [149] patchwork_1.3.2
## [150] bit64_4.6.0-1
## [151] ggplot2_4.0.0
## [152] KEGGREST_1.51.0
## [153] SummarizedExperiment_1.41.0
## [154] AnnotationHub_4.0.0
## [155] igraph_2.2.1
## [156] memoise_2.0.1
## [157] bslib_0.9.0
## [158] ggtree_4.1.1
## [159] fastmatch_1.1-6
## [160] bit_4.6.0
## [161] ape_5.8-1