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 Under development (unstable) (2024-01-16 r85808)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-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_1.7.3 BiocStyle_2.31.0
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.4.0                          
##   [2] BiocIO_1.13.0                          
##   [3] bitops_1.0-7                           
##   [4] ggplotify_0.1.2                        
##   [5] filelock_1.0.3                         
##   [6] tibble_3.2.1                           
##   [7] polyclip_1.10-6                        
##   [8] XML_3.99-0.16.1                        
##   [9] lifecycle_1.0.4                        
##  [10] httr2_1.0.0                            
##  [11] lattice_0.22-5                         
##  [12] MASS_7.3-60.2                          
##  [13] magrittr_2.0.3                         
##  [14] plotly_4.10.4                          
##  [15] sass_0.4.8                             
##  [16] rmarkdown_2.25                         
##  [17] jquerylib_0.1.4                        
##  [18] yaml_2.3.8                             
##  [19] BRGenomics_1.15.0                      
##  [20] plotrix_3.8-4                          
##  [21] cowplot_1.1.3                          
##  [22] DBI_1.2.1                              
##  [23] RColorBrewer_1.1-3                     
##  [24] lubridate_1.9.3                        
##  [25] abind_1.4-5                            
##  [26] zlibbioc_1.49.0                        
##  [27] GenomicRanges_1.55.3                   
##  [28] purrr_1.0.2                            
##  [29] ggraph_2.1.0                           
##  [30] BiocGenerics_0.49.1                    
##  [31] RCurl_1.98-1.14                        
##  [32] yulab.utils_0.1.4                      
##  [33] tweenr_2.0.2                           
##  [34] rappdirs_0.3.3                         
##  [35] GenomeInfoDbData_1.2.11                
##  [36] IRanges_2.37.1                         
##  [37] S4Vectors_0.41.3                       
##  [38] enrichplot_1.23.1                      
##  [39] ggrepel_0.9.5                          
##  [40] tidytree_0.4.6                         
##  [41] ChIPseeker_1.39.0                      
##  [42] codetools_0.2-19                       
##  [43] DelayedArray_0.29.1                    
##  [44] DOSE_3.29.2                            
##  [45] xml2_1.3.6                             
##  [46] ggforce_0.4.1                          
##  [47] tidyselect_1.2.0                       
##  [48] aplot_0.2.2                            
##  [49] farver_2.1.1                           
##  [50] viridis_0.6.5                          
##  [51] base64enc_0.1-3                        
##  [52] matrixStats_1.2.0                      
##  [53] stats4_4.4.0                           
##  [54] BiocFileCache_2.11.1                   
##  [55] GenomicAlignments_1.39.2               
##  [56] jsonlite_1.8.8                         
##  [57] tidygraph_1.3.1                        
##  [58] tools_4.4.0                            
##  [59] progress_1.2.3                         
##  [60] treeio_1.27.0                          
##  [61] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [62] Rcpp_1.0.12                            
##  [63] glue_1.7.0                             
##  [64] gridExtra_2.3                          
##  [65] SparseArray_1.3.4                      
##  [66] xfun_0.42                              
##  [67] DESeq2_1.43.2                          
##  [68] qvalue_2.35.0                          
##  [69] MatrixGenerics_1.15.0                  
##  [70] GenomeInfoDb_1.39.6                    
##  [71] dplyr_1.1.4                            
##  [72] withr_3.0.0                            
##  [73] BiocManager_1.30.22                    
##  [74] fastmap_1.1.1                          
##  [75] boot_1.3-28.1                          
##  [76] fansi_1.0.6                            
##  [77] caTools_1.18.2                         
##  [78] digest_0.6.34                          
##  [79] mime_0.12                              
##  [80] timechange_0.3.0                       
##  [81] R6_2.5.1                               
##  [82] gridGraphics_0.5-1                     
##  [83] seqPattern_1.35.0                      
##  [84] colorspace_2.1-0                       
##  [85] GO.db_3.18.0                           
##  [86] gtools_3.9.5                           
##  [87] biomaRt_2.59.1                         
##  [88] RSQLite_2.3.5                          
##  [89] utf8_1.2.4                             
##  [90] tidyr_1.3.1                            
##  [91] generics_0.1.3                         
##  [92] data.table_1.15.0                      
##  [93] bsplus_0.1.4                           
##  [94] rtracklayer_1.63.0                     
##  [95] htmlwidgets_1.6.4                      
##  [96] prettyunits_1.2.0                      
##  [97] graphlayouts_1.1.0                     
##  [98] httr_1.4.7                             
##  [99] S4Arrays_1.3.3                         
## [100] scatterpie_0.2.1                       
## [101] downloadthis_0.3.3                     
## [102] pkgconfig_2.0.3                        
## [103] gtable_0.3.4                           
## [104] blob_1.2.4                             
## [105] impute_1.77.0                          
## [106] XVector_0.43.1                         
## [107] shadowtext_0.1.3                       
## [108] htmltools_0.5.7                        
## [109] bookdown_0.37                          
## [110] fgsea_1.29.0                           
## [111] scales_1.3.0                           
## [112] Biobase_2.63.0                         
## [113] png_0.1-8                              
## [114] ggfun_0.1.4                            
## [115] knitr_1.45                             
## [116] tzdb_0.4.0                             
## [117] reshape2_1.4.4                         
## [118] rjson_0.2.21                           
## [119] nlme_3.1-164                           
## [120] curl_5.2.0                             
## [121] cachem_1.0.8                           
## [122] stringr_1.5.1                          
## [123] BiocVersion_3.19.1                     
## [124] KernSmooth_2.23-22                     
## [125] parallel_4.4.0                         
## [126] HDO.db_0.99.1                          
## [127] AnnotationDbi_1.65.2                   
## [128] restfulr_0.0.15                        
## [129] pillar_1.9.0                           
## [130] grid_4.4.0                             
## [131] vctrs_0.6.5                            
## [132] gplots_3.1.3.1                         
## [133] dbplyr_2.4.0                           
## [134] evaluate_0.23                          
## [135] magick_2.8.2                           
## [136] readr_2.1.5                            
## [137] GenomicFeatures_1.55.3                 
## [138] cli_3.6.2                              
## [139] locfit_1.5-9.8                         
## [140] compiler_4.4.0                         
## [141] Rsamtools_2.19.3                       
## [142] rlang_1.1.3                            
## [143] crayon_1.5.2                           
## [144] labeling_0.4.3                         
## [145] plyr_1.8.9                             
## [146] fs_1.6.3                               
## [147] stringi_1.8.3                          
## [148] genomation_1.35.0                      
## [149] viridisLite_0.4.2                      
## [150] gridBase_0.4-7                         
## [151] BiocParallel_1.37.0                    
## [152] munsell_0.5.0                          
## [153] Biostrings_2.71.2                      
## [154] lazyeval_0.2.2                         
## [155] GOSemSim_2.29.1                        
## [156] Matrix_1.6-5                           
## [157] BSgenome_1.71.2                        
## [158] hms_1.1.3                              
## [159] patchwork_1.2.0                        
## [160] bit64_4.0.5                            
## [161] ggplot2_3.4.4                          
## [162] KEGGREST_1.43.0                        
## [163] highr_0.10                             
## [164] SummarizedExperiment_1.33.3            
## [165] AnnotationHub_3.11.1                   
## [166] igraph_2.0.1.1                         
## [167] memoise_2.0.1                          
## [168] bslib_0.6.1                            
## [169] ggtree_3.11.0                          
## [170] fastmatch_1.1-4                        
## [171] bit_4.0.5                              
## [172] ape_5.7-1