Contents

0.0.1 EpiArchives is a public archive for interactive HTML reports generated by EpiCompare and the associated code used to create them.

1 Home

1.1 Reports

1.1.1 atac_dnase_chip_example

  • Analysis of ATAC-seq, DNase-seq and ChIP-seq data from K562 cells. All data comes from ENCODE. Only chromosome 1 is analysed in this example.
  • Code to reproduce.

1.1.2 atac_dnase_example

2 Session Information

utils::sessionInfo()
## R version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## 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_1.13.2 BiocStyle_2.37.1 
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.5.1                          
##   [2] BiocIO_1.19.0                          
##   [3] bitops_1.0-9                           
##   [4] ggplotify_0.1.3                        
##   [5] filelock_1.0.3                         
##   [6] tibble_3.3.0                           
##   [7] R.oo_1.27.1                            
##   [8] XML_3.99-0.19                          
##   [9] lifecycle_1.0.4                        
##  [10] httr2_1.2.1                            
##  [11] lattice_0.22-7                         
##  [12] magrittr_2.0.4                         
##  [13] plotly_4.11.0                          
##  [14] sass_0.4.10                            
##  [15] rmarkdown_2.30                         
##  [16] jquerylib_0.1.4                        
##  [17] yaml_2.3.10                            
##  [18] plotrix_3.8-4                          
##  [19] ggtangle_0.0.7                         
##  [20] cowplot_1.2.0                          
##  [21] DBI_1.2.3                              
##  [22] RColorBrewer_1.1-3                     
##  [23] lubridate_1.9.4                        
##  [24] abind_1.4-8                            
##  [25] GenomicRanges_1.61.5                   
##  [26] purrr_1.1.0                            
##  [27] R.utils_2.13.0                         
##  [28] BiocGenerics_0.55.1                    
##  [29] RCurl_1.98-1.17                        
##  [30] yulab.utils_0.2.1                      
##  [31] rappdirs_0.3.3                         
##  [32] gdtools_0.4.4                          
##  [33] IRanges_2.43.5                         
##  [34] S4Vectors_0.47.4                       
##  [35] enrichplot_1.29.2                      
##  [36] ggrepel_0.9.6                          
##  [37] tidytree_0.4.6                         
##  [38] ChIPseeker_1.45.0                      
##  [39] codetools_0.2-20                       
##  [40] DelayedArray_0.35.3                    
##  [41] DOSE_4.3.0                             
##  [42] tidyselect_1.2.1                       
##  [43] aplot_0.2.9                            
##  [44] UCSC.utils_1.5.0                       
##  [45] farver_2.1.2                           
##  [46] base64enc_0.1-3                        
##  [47] matrixStats_1.5.0                      
##  [48] stats4_4.5.1                           
##  [49] BiocFileCache_2.99.6                   
##  [50] Seqinfo_0.99.2                         
##  [51] GenomicAlignments_1.45.4               
##  [52] jsonlite_2.0.0                         
##  [53] systemfonts_1.3.1                      
##  [54] tools_4.5.1                            
##  [55] treeio_1.33.0                          
##  [56] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [57] Rcpp_1.1.0                             
##  [58] glue_1.8.0                             
##  [59] SparseArray_1.9.1                      
##  [60] xfun_0.53                              
##  [61] qvalue_2.41.0                          
##  [62] MatrixGenerics_1.21.0                  
##  [63] GenomeInfoDb_1.45.12                   
##  [64] dplyr_1.1.4                            
##  [65] withr_3.0.2                            
##  [66] BiocManager_1.30.26                    
##  [67] fastmap_1.2.0                          
##  [68] boot_1.3-32                            
##  [69] caTools_1.18.3                         
##  [70] digest_0.6.37                          
##  [71] timechange_0.3.0                       
##  [72] R6_2.6.1                               
##  [73] mime_0.13                              
##  [74] gridGraphics_0.5-1                     
##  [75] seqPattern_1.41.0                      
##  [76] GO.db_3.21.0                           
##  [77] gtools_3.9.5                           
##  [78] dichromat_2.0-0.1                      
##  [79] RSQLite_2.4.3                          
##  [80] R.methodsS3_1.8.2                      
##  [81] tidyr_1.3.1                            
##  [82] generics_0.1.4                         
##  [83] fontLiberation_0.1.0                   
##  [84] data.table_1.17.8                      
##  [85] rtracklayer_1.69.1                     
##  [86] bsplus_0.1.5                           
##  [87] httr_1.4.7                             
##  [88] htmlwidgets_1.6.4                      
##  [89] S4Arrays_1.9.1                         
##  [90] downloadthis_0.5.0                     
##  [91] pkgconfig_2.0.3                        
##  [92] gtable_0.3.6                           
##  [93] blob_1.2.4                             
##  [94] S7_0.2.0                               
##  [95] impute_1.83.0                          
##  [96] XVector_0.49.1                         
##  [97] htmltools_0.5.8.1                      
##  [98] fontBitstreamVera_0.1.1                
##  [99] bookdown_0.45                          
## [100] fgsea_1.35.8                           
## [101] scales_1.4.0                           
## [102] Biobase_2.69.1                         
## [103] png_0.1-8                              
## [104] ggfun_0.2.0                            
## [105] knitr_1.50                             
## [106] tzdb_0.5.0                             
## [107] reshape2_1.4.4                         
## [108] rjson_0.2.23                           
## [109] nlme_3.1-168                           
## [110] curl_7.0.0                             
## [111] cachem_1.1.0                           
## [112] stringr_1.5.2                          
## [113] BiocVersion_3.22.0                     
## [114] KernSmooth_2.23-26                     
## [115] parallel_4.5.1                         
## [116] AnnotationDbi_1.71.1                   
## [117] restfulr_0.0.16                        
## [118] pillar_1.11.1                          
## [119] grid_4.5.1                             
## [120] vctrs_0.6.5                            
## [121] gplots_3.2.0                           
## [122] dbplyr_2.5.1                           
## [123] evaluate_1.0.5                         
## [124] magick_2.9.0                           
## [125] tinytex_0.57                           
## [126] readr_2.1.5                            
## [127] GenomicFeatures_1.61.6                 
## [128] cli_3.6.5                              
## [129] compiler_4.5.1                         
## [130] Rsamtools_2.25.3                       
## [131] rlang_1.1.6                            
## [132] crayon_1.5.3                           
## [133] labeling_0.4.3                         
## [134] plyr_1.8.9                             
## [135] fs_1.6.6                               
## [136] ggiraph_0.9.2                          
## [137] stringi_1.8.7                          
## [138] genomation_1.41.1                      
## [139] viridisLite_0.4.2                      
## [140] gridBase_0.4-7                         
## [141] BiocParallel_1.43.4                    
## [142] Biostrings_2.77.2                      
## [143] lazyeval_0.2.2                         
## [144] GOSemSim_2.35.2                        
## [145] fontquiver_0.2.1                       
## [146] Matrix_1.7-4                           
## [147] BSgenome_1.77.2                        
## [148] hms_1.1.3                              
## [149] patchwork_1.3.2                        
## [150] bit64_4.6.0-1                          
## [151] ggplot2_4.0.0                          
## [152] KEGGREST_1.49.1                        
## [153] SummarizedExperiment_1.39.2            
## [154] AnnotationHub_3.99.6                   
## [155] igraph_2.1.4                           
## [156] memoise_2.0.1                          
## [157] bslib_0.9.0                            
## [158] ggtree_3.99.0                          
## [159] fastmatch_1.1-6                        
## [160] bit_4.6.0                              
## [161] ape_5.8-1