epicompare is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.
First, install Docker if you have not already.
Create an image of the Docker container in command line:
docker pull neurogenomicslab/epicompareOnce 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<your_password> above with whatever you want your password to be.-v flags for your particular use case.-d ensures the container will run in “detached” mode,
which means it will persist even after you’ve closed your command line session.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/epicompareFinally, 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.
utils::sessionInfo()## R Under development (unstable) (2022-12-10 r83428 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] EpiCompare_1.3.0 BiocStyle_2.27.0
##
## loaded via a namespace (and not attached):
## [1] splines_4.3.0
## [2] later_1.3.0
## [3] BiocIO_1.9.1
## [4] bitops_1.0-7
## [5] ggplotify_0.1.0
## [6] filelock_1.0.2
## [7] tibble_3.1.8
## [8] polyclip_1.10-4
## [9] XML_3.99-0.13
## [10] lifecycle_1.0.3
## [11] lattice_0.20-45
## [12] MASS_7.3-58.1
## [13] magrittr_2.0.3
## [14] plotly_4.10.1
## [15] sass_0.4.4
## [16] rmarkdown_2.19
## [17] plotrix_3.8-2
## [18] jquerylib_0.1.4
## [19] yaml_2.3.6
## [20] BRGenomics_1.11.0
## [21] httpuv_1.6.7
## [22] cowplot_1.1.1
## [23] DBI_1.1.3
## [24] RColorBrewer_1.1-3
## [25] zlibbioc_1.45.0
## [26] GenomicRanges_1.51.4
## [27] purrr_0.3.5
## [28] ggraph_2.1.0
## [29] BiocGenerics_0.45.0
## [30] RCurl_1.98-1.9
## [31] yulab.utils_0.0.5
## [32] tweenr_2.0.2
## [33] rappdirs_0.3.3
## [34] GenomeInfoDbData_1.2.9
## [35] IRanges_2.33.0
## [36] S4Vectors_0.37.3
## [37] enrichplot_1.19.1
## [38] ggrepel_0.9.2
## [39] tidytree_0.4.1
## [40] annotate_1.77.0
## [41] ChIPseeker_1.35.0
## [42] codetools_0.2-18
## [43] DelayedArray_0.25.0
## [44] DOSE_3.25.0
## [45] xml2_1.3.3
## [46] ggforce_0.4.1
## [47] tidyselect_1.2.0
## [48] aplot_0.1.9
## [49] farver_2.1.1
## [50] viridis_0.6.2
## [51] matrixStats_0.63.0
## [52] stats4_4.3.0
## [53] BiocFileCache_2.7.1
## [54] GenomicAlignments_1.35.0
## [55] jsonlite_1.8.4
## [56] ellipsis_0.3.2
## [57] tidygraph_1.2.2
## [58] tools_4.3.0
## [59] progress_1.2.2
## [60] treeio_1.23.0
## [61] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [62] Rcpp_1.0.9
## [63] glue_1.6.2
## [64] gridExtra_2.3
## [65] xfun_0.35
## [66] DESeq2_1.39.3
## [67] qvalue_2.31.1
## [68] MatrixGenerics_1.11.0
## [69] GenomeInfoDb_1.35.8
## [70] dplyr_1.0.10
## [71] withr_2.5.0
## [72] BiocManager_1.30.19
## [73] fastmap_1.1.0
## [74] boot_1.3-28.1
## [75] fansi_1.0.3
## [76] caTools_1.18.2
## [77] digest_0.6.31
## [78] R6_2.5.1
## [79] mime_0.12
## [80] gridGraphics_0.5-1
## [81] seqPattern_1.31.0
## [82] colorspace_2.0-3
## [83] GO.db_3.16.0
## [84] gtools_3.9.4
## [85] biomaRt_2.55.0
## [86] RSQLite_2.2.19
## [87] utf8_1.2.2
## [88] tidyr_1.2.1
## [89] generics_0.1.3
## [90] data.table_1.14.6
## [91] rtracklayer_1.59.0
## [92] htmlwidgets_1.6.0
## [93] prettyunits_1.1.1
## [94] graphlayouts_0.8.4
## [95] httr_1.4.4
## [96] scatterpie_0.1.8
## [97] pkgconfig_2.0.3
## [98] gtable_0.3.1
## [99] blob_1.2.3
## [100] impute_1.73.0
## [101] XVector_0.39.0
## [102] shadowtext_0.1.2
## [103] htmltools_0.5.4
## [104] bookdown_0.31
## [105] fgsea_1.25.0
## [106] geneplotter_1.77.0
## [107] scales_1.2.1
## [108] Biobase_2.59.0
## [109] png_0.1-8
## [110] ggfun_0.0.9
## [111] knitr_1.41
## [112] tzdb_0.3.0
## [113] reshape2_1.4.4
## [114] rjson_0.2.21
## [115] nlme_3.1-161
## [116] curl_4.3.3
## [117] cachem_1.0.6
## [118] stringr_1.5.0
## [119] KernSmooth_2.23-20
## [120] BiocVersion_3.17.1
## [121] parallel_4.3.0
## [122] HDO.db_0.99.1
## [123] AnnotationDbi_1.61.0
## [124] restfulr_0.0.15
## [125] pillar_1.8.1
## [126] grid_4.3.0
## [127] vctrs_0.5.1
## [128] gplots_3.1.3
## [129] promises_1.2.0.1
## [130] dbplyr_2.2.1
## [131] xtable_1.8-4
## [132] evaluate_0.19
## [133] magick_2.7.3
## [134] readr_2.1.3
## [135] GenomicFeatures_1.51.4
## [136] cli_3.4.1
## [137] locfit_1.5-9.6
## [138] compiler_4.3.0
## [139] Rsamtools_2.15.0
## [140] rlang_1.0.6
## [141] crayon_1.5.2
## [142] labeling_0.4.2
## [143] plyr_1.8.8
## [144] stringi_1.7.8
## [145] gridBase_0.4-7
## [146] genomation_1.31.0
## [147] viridisLite_0.4.1
## [148] BiocParallel_1.33.7
## [149] assertthat_0.2.1
## [150] munsell_0.5.0
## [151] Biostrings_2.67.0
## [152] lazyeval_0.2.2
## [153] GOSemSim_2.25.0
## [154] Matrix_1.5-3
## [155] BSgenome_1.67.1
## [156] hms_1.1.2
## [157] patchwork_1.1.2
## [158] bit64_4.0.5
## [159] ggplot2_3.4.0
## [160] KEGGREST_1.39.0
## [161] shiny_1.7.4
## [162] highr_0.9
## [163] SummarizedExperiment_1.29.1
## [164] interactiveDisplayBase_1.37.0
## [165] AnnotationHub_3.7.0
## [166] igraph_1.3.5
## [167] memoise_2.0.1
## [168] bslib_0.4.1
## [169] ggtree_3.7.1
## [170] fastmatch_1.1-3
## [171] bit_4.0.5
## [172] ape_5.6-2