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 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-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_1.4.0 BiocStyle_2.28.0
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.3.0                          
##   [2] later_1.3.0                            
##   [3] BiocIO_1.10.0                          
##   [4] bitops_1.0-7                           
##   [5] ggplotify_0.1.0                        
##   [6] filelock_1.0.2                         
##   [7] tibble_3.2.1                           
##   [8] polyclip_1.10-4                        
##   [9] XML_3.99-0.14                          
##  [10] lifecycle_1.0.3                        
##  [11] lattice_0.21-8                         
##  [12] MASS_7.3-59                            
##  [13] magrittr_2.0.3                         
##  [14] plotly_4.10.1                          
##  [15] sass_0.4.5                             
##  [16] rmarkdown_2.21                         
##  [17] jquerylib_0.1.4                        
##  [18] yaml_2.3.7                             
##  [19] BRGenomics_1.12.0                      
##  [20] plotrix_3.8-2                          
##  [21] httpuv_1.6.9                           
##  [22] cowplot_1.1.1                          
##  [23] DBI_1.1.3                              
##  [24] RColorBrewer_1.1-3                     
##  [25] lubridate_1.9.2                        
##  [26] zlibbioc_1.46.0                        
##  [27] GenomicRanges_1.52.0                   
##  [28] purrr_1.0.1                            
##  [29] ggraph_2.1.0                           
##  [30] BiocGenerics_0.46.0                    
##  [31] RCurl_1.98-1.12                        
##  [32] yulab.utils_0.0.6                      
##  [33] tweenr_2.0.2                           
##  [34] rappdirs_0.3.3                         
##  [35] GenomeInfoDbData_1.2.10                
##  [36] IRanges_2.34.0                         
##  [37] S4Vectors_0.38.0                       
##  [38] enrichplot_1.20.0                      
##  [39] ggrepel_0.9.3                          
##  [40] tidytree_0.4.2                         
##  [41] ChIPseeker_1.36.0                      
##  [42] codetools_0.2-19                       
##  [43] DelayedArray_0.26.0                    
##  [44] DOSE_3.26.0                            
##  [45] xml2_1.3.3                             
##  [46] ggforce_0.4.1                          
##  [47] tidyselect_1.2.0                       
##  [48] aplot_0.1.10                           
##  [49] farver_2.1.1                           
##  [50] viridis_0.6.2                          
##  [51] base64enc_0.1-3                        
##  [52] matrixStats_0.63.0                     
##  [53] stats4_4.3.0                           
##  [54] BiocFileCache_2.8.0                    
##  [55] GenomicAlignments_1.36.0               
##  [56] jsonlite_1.8.4                         
##  [57] ellipsis_0.3.2                         
##  [58] tidygraph_1.2.3                        
##  [59] tools_4.3.0                            
##  [60] progress_1.2.2                         
##  [61] treeio_1.24.0                          
##  [62] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [63] Rcpp_1.0.10                            
##  [64] glue_1.6.2                             
##  [65] gridExtra_2.3                          
##  [66] xfun_0.39                              
##  [67] DESeq2_1.40.0                          
##  [68] qvalue_2.32.0                          
##  [69] MatrixGenerics_1.12.0                  
##  [70] GenomeInfoDb_1.36.0                    
##  [71] dplyr_1.1.2                            
##  [72] withr_2.5.0                            
##  [73] BiocManager_1.30.20                    
##  [74] fastmap_1.1.1                          
##  [75] boot_1.3-28.1                          
##  [76] fansi_1.0.4                            
##  [77] caTools_1.18.2                         
##  [78] digest_0.6.31                          
##  [79] timechange_0.2.0                       
##  [80] R6_2.5.1                               
##  [81] mime_0.12                              
##  [82] gridGraphics_0.5-1                     
##  [83] seqPattern_1.32.0                      
##  [84] colorspace_2.1-0                       
##  [85] GO.db_3.17.0                           
##  [86] gtools_3.9.4                           
##  [87] biomaRt_2.56.0                         
##  [88] RSQLite_2.3.1                          
##  [89] utf8_1.2.3                             
##  [90] tidyr_1.3.0                            
##  [91] generics_0.1.3                         
##  [92] data.table_1.14.8                      
##  [93] bsplus_0.1.4                           
##  [94] rtracklayer_1.60.0                     
##  [95] htmlwidgets_1.6.2                      
##  [96] prettyunits_1.1.1                      
##  [97] graphlayouts_0.8.4                     
##  [98] httr_1.4.5                             
##  [99] scatterpie_0.1.9                       
## [100] downloadthis_0.3.2                     
## [101] pkgconfig_2.0.3                        
## [102] gtable_0.3.3                           
## [103] blob_1.2.4                             
## [104] impute_1.74.0                          
## [105] XVector_0.40.0                         
## [106] shadowtext_0.1.2                       
## [107] htmltools_0.5.5                        
## [108] bookdown_0.33                          
## [109] fgsea_1.26.0                           
## [110] scales_1.2.1                           
## [111] Biobase_2.60.0                         
## [112] png_0.1-8                              
## [113] ggfun_0.0.9                            
## [114] knitr_1.42                             
## [115] tzdb_0.3.0                             
## [116] reshape2_1.4.4                         
## [117] rjson_0.2.21                           
## [118] nlme_3.1-162                           
## [119] curl_5.0.0                             
## [120] cachem_1.0.7                           
## [121] stringr_1.5.0                          
## [122] BiocVersion_3.17.1                     
## [123] KernSmooth_2.23-20                     
## [124] parallel_4.3.0                         
## [125] HDO.db_0.99.1                          
## [126] AnnotationDbi_1.62.0                   
## [127] restfulr_0.0.15                        
## [128] pillar_1.9.0                           
## [129] grid_4.3.0                             
## [130] vctrs_0.6.2                            
## [131] gplots_3.1.3                           
## [132] promises_1.2.0.1                       
## [133] dbplyr_2.3.2                           
## [134] xtable_1.8-4                           
## [135] evaluate_0.20                          
## [136] magick_2.7.4                           
## [137] readr_2.1.4                            
## [138] GenomicFeatures_1.52.0                 
## [139] cli_3.6.1                              
## [140] locfit_1.5-9.7                         
## [141] compiler_4.3.0                         
## [142] Rsamtools_2.16.0                       
## [143] rlang_1.1.0                            
## [144] crayon_1.5.2                           
## [145] labeling_0.4.2                         
## [146] fs_1.6.2                               
## [147] plyr_1.8.8                             
## [148] stringi_1.7.12                         
## [149] gridBase_0.4-7                         
## [150] genomation_1.32.0                      
## [151] viridisLite_0.4.1                      
## [152] BiocParallel_1.34.0                    
## [153] munsell_0.5.0                          
## [154] Biostrings_2.68.0                      
## [155] lazyeval_0.2.2                         
## [156] GOSemSim_2.26.0                        
## [157] Matrix_1.5-4                           
## [158] BSgenome_1.68.0                        
## [159] hms_1.1.3                              
## [160] patchwork_1.1.2                        
## [161] bit64_4.0.5                            
## [162] ggplot2_3.4.2                          
## [163] KEGGREST_1.40.0                        
## [164] shiny_1.7.4                            
## [165] highr_0.10                             
## [166] SummarizedExperiment_1.30.0            
## [167] interactiveDisplayBase_1.38.0          
## [168] AnnotationHub_3.8.0                    
## [169] igraph_1.4.2                           
## [170] memoise_2.0.1                          
## [171] bslib_0.4.2                            
## [172] ggtree_3.8.0                           
## [173] fastmatch_1.1-3                        
## [174] bit_4.0.5                              
## [175] ape_5.7-1