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: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## 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_1.2.0                       
##   [3] htmlwidgets_1.5.4                      
##   [4] RSQLite_2.2.18                         
##   [5] AnnotationDbi_1.60.0                   
##   [6] grid_4.2.1                             
##   [7] BiocParallel_1.32.0                    
##   [8] scatterpie_0.1.8                       
##   [9] munsell_0.5.0                          
##  [10] codetools_0.2-18                       
##  [11] withr_2.5.0                            
##  [12] colorspace_2.0-3                       
##  [13] GOSemSim_2.24.0                        
##  [14] Biobase_2.58.0                         
##  [15] filelock_1.0.2                         
##  [16] highr_0.9                              
##  [17] knitr_1.40                             
##  [18] stats4_4.2.1                           
##  [19] DOSE_3.24.0                            
##  [20] labeling_0.4.2                         
##  [21] MatrixGenerics_1.10.0                  
##  [22] GenomeInfoDbData_1.2.9                 
##  [23] polyclip_1.10-4                        
##  [24] seqPattern_1.30.0                      
##  [25] bit64_4.0.5                            
##  [26] farver_2.1.1                           
##  [27] vctrs_0.5.0                            
##  [28] treeio_1.22.0                          
##  [29] generics_0.1.3                         
##  [30] xfun_0.34                              
##  [31] BiocFileCache_2.6.0                    
##  [32] R6_2.5.1                               
##  [33] GenomeInfoDb_1.34.0                    
##  [34] graphlayouts_0.8.3                     
##  [35] locfit_1.5-9.6                         
##  [36] bitops_1.0-7                           
##  [37] BRGenomics_1.10.0                      
##  [38] cachem_1.0.6                           
##  [39] fgsea_1.24.0                           
##  [40] gridGraphics_0.5-1                     
##  [41] DelayedArray_0.24.0                    
##  [42] assertthat_0.2.1                       
##  [43] promises_1.2.0.1                       
##  [44] BiocIO_1.8.0                           
##  [45] scales_1.2.1                           
##  [46] ggraph_2.1.0                           
##  [47] enrichplot_1.18.0                      
##  [48] gtable_0.3.1                           
##  [49] tidygraph_1.2.2                        
##  [50] rlang_1.0.6                            
##  [51] genefilter_1.80.0                      
##  [52] splines_4.2.1                          
##  [53] rtracklayer_1.58.0                     
##  [54] lazyeval_0.2.2                         
##  [55] impute_1.72.0                          
##  [56] BiocManager_1.30.19                    
##  [57] yaml_2.3.6                             
##  [58] reshape2_1.4.4                         
##  [59] GenomicFeatures_1.50.0                 
##  [60] httpuv_1.6.6                           
##  [61] qvalue_2.30.0                          
##  [62] tools_4.2.1                            
##  [63] bookdown_0.29                          
##  [64] ggplotify_0.1.0                        
##  [65] gridBase_0.4-7                         
##  [66] ggplot2_3.3.6                          
##  [67] ellipsis_0.3.2                         
##  [68] gplots_3.1.3                           
##  [69] jquerylib_0.1.4                        
##  [70] RColorBrewer_1.1-3                     
##  [71] BiocGenerics_0.44.0                    
##  [72] Rcpp_1.0.9                             
##  [73] plyr_1.8.7                             
##  [74] progress_1.2.2                         
##  [75] zlibbioc_1.44.0                        
##  [76] purrr_0.3.5                            
##  [77] RCurl_1.98-1.9                         
##  [78] prettyunits_1.1.1                      
##  [79] viridis_0.6.2                          
##  [80] cowplot_1.1.1                          
##  [81] S4Vectors_0.36.0                       
##  [82] SummarizedExperiment_1.28.0            
##  [83] ggrepel_0.9.1                          
##  [84] magrittr_2.0.3                         
##  [85] magick_2.7.3                           
##  [86] data.table_1.14.4                      
##  [87] matrixStats_0.62.0                     
##  [88] hms_1.1.2                              
##  [89] patchwork_1.1.2                        
##  [90] mime_0.12                              
##  [91] evaluate_0.17                          
##  [92] xtable_1.8-4                           
##  [93] HDO.db_0.99.1                          
##  [94] XML_3.99-0.12                          
##  [95] IRanges_2.32.0                         
##  [96] gridExtra_2.3                          
##  [97] compiler_4.2.1                         
##  [98] biomaRt_2.54.0                         
##  [99] tibble_3.1.8                           
## [100] KernSmooth_2.23-20                     
## [101] crayon_1.5.2                           
## [102] shadowtext_0.1.2                       
## [103] htmltools_0.5.3                        
## [104] ggfun_0.0.7                            
## [105] later_1.3.0                            
## [106] tzdb_0.3.0                             
## [107] tidyr_1.2.1                            
## [108] geneplotter_1.76.0                     
## [109] aplot_0.1.8                            
## [110] DBI_1.1.3                              
## [111] tweenr_2.0.2                           
## [112] ChIPseeker_1.34.0                      
## [113] genomation_1.30.0                      
## [114] dbplyr_2.2.1                           
## [115] MASS_7.3-58.1                          
## [116] rappdirs_0.3.3                         
## [117] boot_1.3-28                            
## [118] Matrix_1.5-1                           
## [119] readr_2.1.3                            
## [120] cli_3.4.1                              
## [121] parallel_4.2.1                         
## [122] igraph_1.3.5                           
## [123] GenomicRanges_1.50.0                   
## [124] pkgconfig_2.0.3                        
## [125] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [126] GenomicAlignments_1.34.0               
## [127] plotly_4.10.0                          
## [128] xml2_1.3.3                             
## [129] ggtree_3.6.0                           
## [130] annotate_1.76.0                        
## [131] bslib_0.4.0                            
## [132] XVector_0.38.0                         
## [133] yulab.utils_0.0.5                      
## [134] stringr_1.4.1                          
## [135] digest_0.6.30                          
## [136] Biostrings_2.66.0                      
## [137] rmarkdown_2.17                         
## [138] fastmatch_1.1-3                        
## [139] tidytree_0.4.1                         
## [140] restfulr_0.0.15                        
## [141] curl_4.3.3                             
## [142] shiny_1.7.3                            
## [143] Rsamtools_2.14.0                       
## [144] gtools_3.9.3                           
## [145] rjson_0.2.21                           
## [146] lifecycle_1.0.3                        
## [147] nlme_3.1-160                           
## [148] jsonlite_1.8.3                         
## [149] viridisLite_0.4.1                      
## [150] BSgenome_1.66.0                        
## [151] fansi_1.0.3                            
## [152] pillar_1.8.1                           
## [153] lattice_0.20-45                        
## [154] KEGGREST_1.38.0                        
## [155] fastmap_1.1.0                          
## [156] httr_1.4.4                             
## [157] plotrix_3.8-2                          
## [158] survival_3.4-0                         
## [159] GO.db_3.16.0                           
## [160] interactiveDisplayBase_1.36.0          
## [161] glue_1.6.2                             
## [162] png_0.1-7                              
## [163] BiocVersion_3.16.0                     
## [164] bit_4.0.4                              
## [165] ggforce_0.4.1                          
## [166] stringi_1.7.8                          
## [167] sass_0.4.2                             
## [168] blob_1.2.3                             
## [169] DESeq2_1.38.0                          
## [170] AnnotationHub_3.6.0                    
## [171] caTools_1.18.2                         
## [172] memoise_2.0.1                          
## [173] dplyr_1.0.10                           
## [174] ape_5.6-2