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 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] EpiCompare_1.2.0 BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2                             
##   [2] tidyselect_1.1.2                       
##   [3] htmlwidgets_1.5.4                      
##   [4] RSQLite_2.2.14                         
##   [5] AnnotationDbi_1.60.0                   
##   [6] grid_4.2.1                             
##   [7] BiocParallel_1.32.1                    
##   [8] scatterpie_0.1.7                       
##   [9] munsell_0.5.0                          
##  [10] codetools_0.2-18                       
##  [11] colorspace_2.0-3                       
##  [12] GOSemSim_2.24.0                        
##  [13] Biobase_2.58.0                         
##  [14] filelock_1.0.2                         
##  [15] highr_0.9                              
##  [16] knitr_1.39                             
##  [17] stats4_4.2.1                           
##  [18] DOSE_3.24.1                            
##  [19] labeling_0.4.2                         
##  [20] MatrixGenerics_1.10.0                  
##  [21] GenomeInfoDbData_1.2.8                 
##  [22] polyclip_1.10-0                        
##  [23] seqPattern_1.30.0                      
##  [24] bit64_4.0.5                            
##  [25] farver_2.1.1                           
##  [26] vctrs_0.4.1                            
##  [27] treeio_1.22.0                          
##  [28] generics_0.1.3                         
##  [29] xfun_0.31                              
##  [30] BiocFileCache_2.6.0                    
##  [31] R6_2.5.1                               
##  [32] GenomeInfoDb_1.34.2                    
##  [33] graphlayouts_0.8.0                     
##  [34] locfit_1.5-9.6                         
##  [35] bitops_1.0-7                           
##  [36] BRGenomics_1.10.0                      
##  [37] cachem_1.0.6                           
##  [38] fgsea_1.24.0                           
##  [39] gridGraphics_0.5-1                     
##  [40] DelayedArray_0.24.0                    
##  [41] assertthat_0.2.1                       
##  [42] promises_1.2.0.1                       
##  [43] BiocIO_1.8.0                           
##  [44] scales_1.2.0                           
##  [45] ggraph_2.0.5                           
##  [46] enrichplot_1.18.0                      
##  [47] gtable_0.3.0                           
##  [48] tidygraph_1.2.1                        
##  [49] rlang_1.0.4                            
##  [50] genefilter_1.80.0                      
##  [51] splines_4.2.1                          
##  [52] rtracklayer_1.58.0                     
##  [53] lazyeval_0.2.2                         
##  [54] impute_1.72.0                          
##  [55] BiocManager_1.30.18                    
##  [56] yaml_2.3.5                             
##  [57] reshape2_1.4.4                         
##  [58] GenomicFeatures_1.50.2                 
##  [59] httpuv_1.6.5                           
##  [60] qvalue_2.30.0                          
##  [61] tools_4.2.1                            
##  [62] bookdown_0.27                          
##  [63] ggplotify_0.1.0                        
##  [64] gridBase_0.4-7                         
##  [65] ggplot2_3.3.6                          
##  [66] ellipsis_0.3.2                         
##  [67] gplots_3.1.3                           
##  [68] jquerylib_0.1.4                        
##  [69] RColorBrewer_1.1-3                     
##  [70] BiocGenerics_0.44.0                    
##  [71] Rcpp_1.0.9                             
##  [72] plyr_1.8.7                             
##  [73] progress_1.2.2                         
##  [74] zlibbioc_1.44.0                        
##  [75] purrr_0.3.4                            
##  [76] RCurl_1.98-1.7                         
##  [77] prettyunits_1.1.1                      
##  [78] viridis_0.6.2                          
##  [79] cowplot_1.1.1                          
##  [80] S4Vectors_0.36.0                       
##  [81] SummarizedExperiment_1.28.0            
##  [82] ggrepel_0.9.1                          
##  [83] magrittr_2.0.3                         
##  [84] magick_2.7.3                           
##  [85] data.table_1.14.2                      
##  [86] matrixStats_0.62.0                     
##  [87] hms_1.1.1                              
##  [88] patchwork_1.1.1                        
##  [89] mime_0.12                              
##  [90] evaluate_0.15                          
##  [91] xtable_1.8-4                           
##  [92] HDO.db_0.99.1                          
##  [93] XML_3.99-0.10                          
##  [94] IRanges_2.32.0                         
##  [95] gridExtra_2.3                          
##  [96] compiler_4.2.1                         
##  [97] biomaRt_2.54.0                         
##  [98] tibble_3.1.7                           
##  [99] KernSmooth_2.23-20                     
## [100] crayon_1.5.1                           
## [101] shadowtext_0.1.2                       
## [102] htmltools_0.5.2                        
## [103] ggfun_0.0.6                            
## [104] later_1.3.0                            
## [105] tzdb_0.3.0                             
## [106] tidyr_1.2.0                            
## [107] geneplotter_1.76.0                     
## [108] aplot_0.1.6                            
## [109] DBI_1.1.3                              
## [110] tweenr_1.0.2                           
## [111] ChIPseeker_1.34.0                      
## [112] genomation_1.30.0                      
## [113] dbplyr_2.2.1                           
## [114] MASS_7.3-58                            
## [115] rappdirs_0.3.3                         
## [116] boot_1.3-28                            
## [117] Matrix_1.4-1                           
## [118] readr_2.1.2                            
## [119] cli_3.3.0                              
## [120] parallel_4.2.1                         
## [121] igraph_1.3.5                           
## [122] GenomicRanges_1.50.1                   
## [123] pkgconfig_2.0.3                        
## [124] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [125] GenomicAlignments_1.34.0               
## [126] plotly_4.10.0                          
## [127] xml2_1.3.3                             
## [128] ggtree_3.6.0                           
## [129] annotate_1.76.0                        
## [130] bslib_0.3.1                            
## [131] XVector_0.38.0                         
## [132] yulab.utils_0.0.5                      
## [133] stringr_1.4.0                          
## [134] digest_0.6.29                          
## [135] Biostrings_2.66.0                      
## [136] rmarkdown_2.14                         
## [137] fastmatch_1.1-3                        
## [138] tidytree_0.3.9                         
## [139] restfulr_0.0.15                        
## [140] curl_4.3.2                             
## [141] shiny_1.7.1                            
## [142] Rsamtools_2.14.0                       
## [143] gtools_3.9.3                           
## [144] rjson_0.2.21                           
## [145] lifecycle_1.0.1                        
## [146] nlme_3.1-158                           
## [147] jsonlite_1.8.0                         
## [148] viridisLite_0.4.0                      
## [149] BSgenome_1.66.1                        
## [150] fansi_1.0.3                            
## [151] pillar_1.7.0                           
## [152] lattice_0.20-45                        
## [153] KEGGREST_1.38.0                        
## [154] fastmap_1.1.0                          
## [155] httr_1.4.3                             
## [156] plotrix_3.8-2                          
## [157] survival_3.3-1                         
## [158] GO.db_3.15.0                           
## [159] interactiveDisplayBase_1.36.0          
## [160] glue_1.6.2                             
## [161] png_0.1-7                              
## [162] BiocVersion_3.16.0                     
## [163] bit_4.0.4                              
## [164] ggforce_0.3.3                          
## [165] stringi_1.7.8                          
## [166] sass_0.4.1                             
## [167] blob_1.2.3                             
## [168] DESeq2_1.38.0                          
## [169] AnnotationHub_3.6.0                    
## [170] caTools_1.18.2                         
## [171] memoise_2.0.1                          
## [172] dplyr_1.0.9                            
## [173] ape_5.6-2