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 4.3.3 (2024-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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_1.6.7 BiocStyle_2.30.0
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.3                          
##   [2] later_1.3.2                            
##   [3] BiocIO_1.12.0                          
##   [4] bitops_1.0-7                           
##   [5] ggplotify_0.1.2                        
##   [6] filelock_1.0.3                         
##   [7] tibble_3.2.1                           
##   [8] polyclip_1.10-6                        
##   [9] XML_3.99-0.16.1                        
##  [10] lifecycle_1.0.4                        
##  [11] lattice_0.22-6                         
##  [12] MASS_7.3-60.0.1                        
##  [13] magrittr_2.0.3                         
##  [14] plotly_4.10.4                          
##  [15] sass_0.4.9                             
##  [16] rmarkdown_2.26                         
##  [17] plotrix_3.8-4                          
##  [18] jquerylib_0.1.4                        
##  [19] yaml_2.3.8                             
##  [20] BRGenomics_1.14.1                      
##  [21] httpuv_1.6.14                          
##  [22] cowplot_1.1.3                          
##  [23] DBI_1.2.2                              
##  [24] RColorBrewer_1.1-3                     
##  [25] lubridate_1.9.3                        
##  [26] abind_1.4-5                            
##  [27] zlibbioc_1.48.2                        
##  [28] GenomicRanges_1.54.1                   
##  [29] purrr_1.0.2                            
##  [30] ggraph_2.2.1                           
##  [31] BiocGenerics_0.48.1                    
##  [32] RCurl_1.98-1.14                        
##  [33] yulab.utils_0.1.4                      
##  [34] tweenr_2.0.3                           
##  [35] rappdirs_0.3.3                         
##  [36] GenomeInfoDbData_1.2.11                
##  [37] IRanges_2.36.0                         
##  [38] S4Vectors_0.40.2                       
##  [39] enrichplot_1.22.0                      
##  [40] ggrepel_0.9.5                          
##  [41] tidytree_0.4.6                         
##  [42] ChIPseeker_1.38.0                      
##  [43] codetools_0.2-19                       
##  [44] DelayedArray_0.28.0                    
##  [45] DOSE_3.28.2                            
##  [46] xml2_1.3.6                             
##  [47] ggforce_0.4.2                          
##  [48] tidyselect_1.2.1                       
##  [49] aplot_0.2.2                            
##  [50] farver_2.1.1                           
##  [51] viridis_0.6.5                          
##  [52] base64enc_0.1-3                        
##  [53] matrixStats_1.2.0                      
##  [54] stats4_4.3.3                           
##  [55] BiocFileCache_2.10.1                   
##  [56] GenomicAlignments_1.38.2               
##  [57] jsonlite_1.8.8                         
##  [58] ellipsis_0.3.2                         
##  [59] tidygraph_1.3.1                        
##  [60] tools_4.3.3                            
##  [61] progress_1.2.3                         
##  [62] treeio_1.26.0                          
##  [63] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [64] Rcpp_1.0.12                            
##  [65] glue_1.7.0                             
##  [66] gridExtra_2.3                          
##  [67] SparseArray_1.2.4                      
##  [68] xfun_0.42                              
##  [69] DESeq2_1.42.1                          
##  [70] qvalue_2.34.0                          
##  [71] MatrixGenerics_1.14.0                  
##  [72] GenomeInfoDb_1.38.8                    
##  [73] dplyr_1.1.4                            
##  [74] withr_3.0.0                            
##  [75] BiocManager_1.30.22                    
##  [76] fastmap_1.1.1                          
##  [77] boot_1.3-30                            
##  [78] fansi_1.0.6                            
##  [79] caTools_1.18.2                         
##  [80] digest_0.6.35                          
##  [81] timechange_0.3.0                       
##  [82] R6_2.5.1                               
##  [83] mime_0.12                              
##  [84] gridGraphics_0.5-1                     
##  [85] seqPattern_1.34.0                      
##  [86] colorspace_2.1-0                       
##  [87] GO.db_3.18.0                           
##  [88] gtools_3.9.5                           
##  [89] biomaRt_2.58.2                         
##  [90] RSQLite_2.3.5                          
##  [91] utf8_1.2.4                             
##  [92] tidyr_1.3.1                            
##  [93] generics_0.1.3                         
##  [94] data.table_1.15.2                      
##  [95] bsplus_0.1.4                           
##  [96] rtracklayer_1.62.0                     
##  [97] htmlwidgets_1.6.4                      
##  [98] prettyunits_1.2.0                      
##  [99] graphlayouts_1.1.1                     
## [100] httr_1.4.7                             
## [101] S4Arrays_1.2.1                         
## [102] downloadthis_0.3.3                     
## [103] scatterpie_0.2.1                       
## [104] pkgconfig_2.0.3                        
## [105] gtable_0.3.4                           
## [106] blob_1.2.4                             
## [107] impute_1.76.0                          
## [108] XVector_0.42.0                         
## [109] shadowtext_0.1.3                       
## [110] htmltools_0.5.7                        
## [111] bookdown_0.38                          
## [112] fgsea_1.28.0                           
## [113] scales_1.3.0                           
## [114] Biobase_2.62.0                         
## [115] png_0.1-8                              
## [116] ggfun_0.1.4                            
## [117] knitr_1.45                             
## [118] tzdb_0.4.0                             
## [119] reshape2_1.4.4                         
## [120] rjson_0.2.21                           
## [121] nlme_3.1-164                           
## [122] curl_5.2.1                             
## [123] cachem_1.0.8                           
## [124] stringr_1.5.1                          
## [125] KernSmooth_2.23-22                     
## [126] BiocVersion_3.18.1                     
## [127] parallel_4.3.3                         
## [128] HDO.db_0.99.1                          
## [129] AnnotationDbi_1.64.1                   
## [130] restfulr_0.0.15                        
## [131] pillar_1.9.0                           
## [132] grid_4.3.3                             
## [133] vctrs_0.6.5                            
## [134] gplots_3.1.3.1                         
## [135] promises_1.2.1                         
## [136] dbplyr_2.5.0                           
## [137] xtable_1.8-4                           
## [138] evaluate_0.23                          
## [139] magick_2.8.3                           
## [140] readr_2.1.5                            
## [141] GenomicFeatures_1.54.4                 
## [142] cli_3.6.2                              
## [143] locfit_1.5-9.9                         
## [144] compiler_4.3.3                         
## [145] Rsamtools_2.18.0                       
## [146] rlang_1.1.3                            
## [147] crayon_1.5.2                           
## [148] labeling_0.4.3                         
## [149] plyr_1.8.9                             
## [150] fs_1.6.3                               
## [151] stringi_1.8.3                          
## [152] gridBase_0.4-7                         
## [153] genomation_1.34.0                      
## [154] viridisLite_0.4.2                      
## [155] BiocParallel_1.36.0                    
## [156] munsell_0.5.0                          
## [157] Biostrings_2.70.3                      
## [158] lazyeval_0.2.2                         
## [159] GOSemSim_2.28.1                        
## [160] Matrix_1.6-5                           
## [161] BSgenome_1.70.2                        
## [162] hms_1.1.3                              
## [163] patchwork_1.2.0                        
## [164] bit64_4.0.5                            
## [165] ggplot2_3.5.0                          
## [166] KEGGREST_1.42.0                        
## [167] shiny_1.8.0                            
## [168] highr_0.10                             
## [169] SummarizedExperiment_1.32.0            
## [170] interactiveDisplayBase_1.40.0          
## [171] AnnotationHub_3.10.0                   
## [172] igraph_2.0.3                           
## [173] memoise_2.0.1                          
## [174] bslib_0.6.1                            
## [175] ggtree_3.10.1                          
## [176] fastmatch_1.1-4                        
## [177] bit_4.0.5                              
## [178] ape_5.7-1