DockerHub

epicompare is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.

Installation

Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

docker pull neurogenomicslab/epicompare

Once 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

NOTES

  • Make sure to replace <your_password> above with whatever you want your password to be.
  • Change the paths supplied to the -v flags for your particular use case.
  • The -d ensures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
  • The username will be “rstudio” by default.
  • Optionally, you can also install the Docker Desktop to easily manage your containers.

Method 2: via Singularity

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/epicompare

Usage

Finally, 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.

Session Info

utils::sessionInfo()
## R version 4.5.1 (2025-06-13)
## 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] EpiCompare_1.12.2 BiocStyle_2.36.0 
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3                     
##   [2] jsonlite_2.0.0                         
##   [3] magrittr_2.0.4                         
##   [4] ggtangle_0.0.7                         
##   [5] GenomicFeatures_1.60.0                 
##   [6] farver_2.1.2                           
##   [7] rmarkdown_2.30                         
##   [8] fs_1.6.6                               
##   [9] BiocIO_1.18.0                          
##  [10] ragg_1.5.0                             
##  [11] vctrs_0.6.5                            
##  [12] memoise_2.0.1                          
##  [13] Rsamtools_2.24.1                       
##  [14] RCurl_1.98-1.17                        
##  [15] ggtree_3.16.3                          
##  [16] htmltools_0.5.8.1                      
##  [17] S4Arrays_1.8.1                         
##  [18] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [19] plotrix_3.8-4                          
##  [20] AnnotationHub_3.16.1                   
##  [21] curl_7.0.0                             
##  [22] SparseArray_1.8.1                      
##  [23] gridGraphics_0.5-1                     
##  [24] sass_0.4.10                            
##  [25] KernSmooth_2.23-26                     
##  [26] bslib_0.9.0                            
##  [27] htmlwidgets_1.6.4                      
##  [28] desc_1.4.3                             
##  [29] plyr_1.8.9                             
##  [30] plotly_4.11.0                          
##  [31] impute_1.82.0                          
##  [32] cachem_1.1.0                           
##  [33] GenomicAlignments_1.44.0               
##  [34] igraph_2.1.4                           
##  [35] downloadthis_0.5.0                     
##  [36] lifecycle_1.0.4                        
##  [37] pkgconfig_2.0.3                        
##  [38] Matrix_1.7-4                           
##  [39] R6_2.6.1                               
##  [40] fastmap_1.2.0                          
##  [41] GenomeInfoDbData_1.2.14                
##  [42] MatrixGenerics_1.20.0                  
##  [43] digest_0.6.37                          
##  [44] aplot_0.2.9                            
##  [45] enrichplot_1.28.4                      
##  [46] patchwork_1.3.2                        
##  [47] AnnotationDbi_1.70.0                   
##  [48] S4Vectors_0.46.0                       
##  [49] textshaping_1.0.3                      
##  [50] GenomicRanges_1.60.0                   
##  [51] RSQLite_2.4.3                          
##  [52] filelock_1.0.3                         
##  [53] httr_1.4.7                             
##  [54] abind_1.4-8                            
##  [55] compiler_4.5.1                         
##  [56] bit64_4.6.0-1                          
##  [57] S7_0.2.0                               
##  [58] BiocParallel_1.42.2                    
##  [59] DBI_1.2.3                              
##  [60] gplots_3.2.0                           
##  [61] R.utils_2.13.0                         
##  [62] ChIPseeker_1.44.0                      
##  [63] rappdirs_0.3.3                         
##  [64] DelayedArray_0.34.1                    
##  [65] rjson_0.2.23                           
##  [66] caTools_1.18.3                         
##  [67] gtools_3.9.5                           
##  [68] tools_4.5.1                            
##  [69] ape_5.8-1                              
##  [70] R.oo_1.27.1                            
##  [71] glue_1.8.0                             
##  [72] restfulr_0.0.16                        
##  [73] nlme_3.1-168                           
##  [74] GOSemSim_2.34.0                        
##  [75] grid_4.5.1                             
##  [76] gridBase_0.4-7                         
##  [77] reshape2_1.4.4                         
##  [78] fgsea_1.34.2                           
##  [79] generics_0.1.4                         
##  [80] BSgenome_1.76.0                        
##  [81] gtable_0.3.6                           
##  [82] tzdb_0.5.0                             
##  [83] R.methodsS3_1.8.2                      
##  [84] seqPattern_1.40.0                      
##  [85] tidyr_1.3.1                            
##  [86] hms_1.1.3                              
##  [87] data.table_1.17.8                      
##  [88] XVector_0.48.0                         
##  [89] BiocGenerics_0.54.0                    
##  [90] ggrepel_0.9.6                          
##  [91] BiocVersion_3.21.1                     
##  [92] pillar_1.11.1                          
##  [93] stringr_1.5.2                          
##  [94] yulab.utils_0.2.1                      
##  [95] splines_4.5.1                          
##  [96] dplyr_1.1.4                            
##  [97] treeio_1.32.0                          
##  [98] BiocFileCache_2.16.2                   
##  [99] lattice_0.22-7                         
## [100] rtracklayer_1.68.0                     
## [101] bit_4.6.0                              
## [102] tidyselect_1.2.1                       
## [103] GO.db_3.21.0                           
## [104] Biostrings_2.76.0                      
## [105] knitr_1.50                             
## [106] bookdown_0.44                          
## [107] IRanges_2.42.0                         
## [108] SummarizedExperiment_1.38.1            
## [109] stats4_4.5.1                           
## [110] xfun_0.53                              
## [111] Biobase_2.68.0                         
## [112] matrixStats_1.5.0                      
## [113] stringi_1.8.7                          
## [114] UCSC.utils_1.4.0                       
## [115] lazyeval_0.2.2                         
## [116] ggfun_0.2.0                            
## [117] yaml_2.3.10                            
## [118] boot_1.3-32                            
## [119] evaluate_1.0.5                         
## [120] codetools_0.2-20                       
## [121] tibble_3.3.0                           
## [122] qvalue_2.40.0                          
## [123] BiocManager_1.30.26                    
## [124] ggplotify_0.1.3                        
## [125] cli_3.6.5                              
## [126] systemfonts_1.2.3                      
## [127] jquerylib_0.1.4                        
## [128] Rcpp_1.1.0                             
## [129] GenomeInfoDb_1.44.3                    
## [130] dbplyr_2.5.1                           
## [131] png_0.1-8                              
## [132] XML_3.99-0.19                          
## [133] parallel_4.5.1                         
## [134] readr_2.1.5                            
## [135] pkgdown_2.1.3                          
## [136] ggplot2_4.0.0                          
## [137] blob_1.2.4                             
## [138] DOSE_4.2.0                             
## [139] bitops_1.0-9                           
## [140] viridisLite_0.4.2                      
## [141] tidytree_0.4.6                         
## [142] scales_1.4.0                           
## [143] genomation_1.40.1                      
## [144] purrr_1.1.0                            
## [145] crayon_1.5.3                           
## [146] rlang_1.1.6                            
## [147] cowplot_1.2.0                          
## [148] fastmatch_1.1-6                        
## [149] KEGGREST_1.48.1