Contents

1 DockerHub

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

1.1 Installation

1.2 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

1.2.1 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.

1.3 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

1.4 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.

2 Session Info

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:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] EpiCompare_1.13.1 BiocStyle_2.37.0 
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3                     
##   [2] jsonlite_2.0.0                         
##   [3] magrittr_2.0.3                         
##   [4] magick_2.8.7                           
##   [5] ggtangle_0.0.7                         
##   [6] GenomicFeatures_1.61.5                 
##   [7] farver_2.1.2                           
##   [8] rmarkdown_2.29                         
##   [9] fs_1.6.6                               
##  [10] BiocIO_1.19.0                          
##  [11] vctrs_0.6.5                            
##  [12] memoise_2.0.1                          
##  [13] Rsamtools_2.25.1                       
##  [14] RCurl_1.98-1.17                        
##  [15] base64enc_0.1-3                        
##  [16] ggtree_3.17.1                          
##  [17] tinytex_0.57                           
##  [18] htmltools_0.5.8.1                      
##  [19] S4Arrays_1.9.1                         
##  [20] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [21] plotrix_3.8-4                          
##  [22] AnnotationHub_3.99.6                   
##  [23] curl_6.4.0                             
##  [24] SparseArray_1.9.1                      
##  [25] gridGraphics_0.5-1                     
##  [26] sass_0.4.10                            
##  [27] KernSmooth_2.23-26                     
##  [28] bslib_0.9.0                            
##  [29] htmlwidgets_1.6.4                      
##  [30] plyr_1.8.9                             
##  [31] httr2_1.2.1                            
##  [32] lubridate_1.9.4                        
##  [33] plotly_4.11.0                          
##  [34] impute_1.83.0                          
##  [35] cachem_1.1.0                           
##  [36] GenomicAlignments_1.45.1               
##  [37] igraph_2.1.4                           
##  [38] mime_0.13                              
##  [39] downloadthis_0.5.0                     
##  [40] lifecycle_1.0.4                        
##  [41] pkgconfig_2.0.3                        
##  [42] Matrix_1.7-3                           
##  [43] R6_2.6.1                               
##  [44] fastmap_1.2.0                          
##  [45] MatrixGenerics_1.21.0                  
##  [46] digest_0.6.37                          
##  [47] aplot_0.2.8                            
##  [48] enrichplot_1.29.2                      
##  [49] patchwork_1.3.1                        
##  [50] AnnotationDbi_1.71.0                   
##  [51] S4Vectors_0.47.0                       
##  [52] GenomicRanges_1.61.1                   
##  [53] RSQLite_2.4.2                          
##  [54] labeling_0.4.3                         
##  [55] bsplus_0.1.5                           
##  [56] filelock_1.0.3                         
##  [57] timechange_0.3.0                       
##  [58] httr_1.4.7                             
##  [59] abind_1.4-8                            
##  [60] compiler_4.5.1                         
##  [61] withr_3.0.2                            
##  [62] bit64_4.6.0-1                          
##  [63] BiocParallel_1.43.4                    
##  [64] DBI_1.2.3                              
##  [65] gplots_3.2.0                           
##  [66] R.utils_2.13.0                         
##  [67] ChIPseeker_1.45.0                      
##  [68] rappdirs_0.3.3                         
##  [69] DelayedArray_0.35.2                    
##  [70] rjson_0.2.23                           
##  [71] caTools_1.18.3                         
##  [72] gtools_3.9.5                           
##  [73] tools_4.5.1                            
##  [74] ape_5.8-1                              
##  [75] R.oo_1.27.1                            
##  [76] glue_1.8.0                             
##  [77] restfulr_0.0.16                        
##  [78] nlme_3.1-168                           
##  [79] GOSemSim_2.35.0                        
##  [80] grid_4.5.1                             
##  [81] gridBase_0.4-7                         
##  [82] reshape2_1.4.4                         
##  [83] fgsea_1.35.6                           
##  [84] generics_0.1.4                         
##  [85] BSgenome_1.77.1                        
##  [86] gtable_0.3.6                           
##  [87] tzdb_0.5.0                             
##  [88] R.methodsS3_1.8.2                      
##  [89] seqPattern_1.41.0                      
##  [90] tidyr_1.3.1                            
##  [91] hms_1.1.3                              
##  [92] data.table_1.17.8                      
##  [93] XVector_0.49.0                         
##  [94] BiocGenerics_0.55.0                    
##  [95] ggrepel_0.9.6                          
##  [96] BiocVersion_3.22.0                     
##  [97] pillar_1.11.0                          
##  [98] stringr_1.5.1                          
##  [99] yulab.utils_0.2.0                      
## [100] splines_4.5.1                          
## [101] dplyr_1.1.4                            
## [102] treeio_1.33.0                          
## [103] BiocFileCache_2.99.5                   
## [104] lattice_0.22-7                         
## [105] rtracklayer_1.69.1                     
## [106] bit_4.6.0                              
## [107] tidyselect_1.2.1                       
## [108] GO.db_3.21.0                           
## [109] Biostrings_2.77.2                      
## [110] knitr_1.50                             
## [111] bookdown_0.43                          
## [112] IRanges_2.43.0                         
## [113] Seqinfo_0.99.2                         
## [114] SummarizedExperiment_1.39.1            
## [115] stats4_4.5.1                           
## [116] xfun_0.52                              
## [117] Biobase_2.69.0                         
## [118] matrixStats_1.5.0                      
## [119] stringi_1.8.7                          
## [120] UCSC.utils_1.5.0                       
## [121] lazyeval_0.2.2                         
## [122] ggfun_0.2.0                            
## [123] yaml_2.3.10                            
## [124] boot_1.3-31                            
## [125] evaluate_1.0.4                         
## [126] codetools_0.2-20                       
## [127] tibble_3.3.0                           
## [128] qvalue_2.41.0                          
## [129] BiocManager_1.30.26                    
## [130] ggplotify_0.1.2                        
## [131] cli_3.6.5                              
## [132] jquerylib_0.1.4                        
## [133] dichromat_2.0-0.1                      
## [134] Rcpp_1.1.0                             
## [135] GenomeInfoDb_1.45.9                    
## [136] dbplyr_2.5.0                           
## [137] png_0.1-8                              
## [138] XML_3.99-0.18                          
## [139] parallel_4.5.1                         
## [140] readr_2.1.5                            
## [141] ggplot2_3.5.2                          
## [142] blob_1.2.4                             
## [143] DOSE_4.3.0                             
## [144] bitops_1.0-9                           
## [145] viridisLite_0.4.2                      
## [146] tidytree_0.4.6                         
## [147] scales_1.4.0                           
## [148] genomation_1.41.0                      
## [149] purrr_1.1.0                            
## [150] crayon_1.5.3                           
## [151] rlang_1.1.6                            
## [152] cowplot_1.2.0                          
## [153] fastmatch_1.1-6                        
## [154] KEGGREST_1.49.1