Example report


Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts


Vignette updated: Apr-25-2024

Source: vignettes/example_report.Rmd

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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.

atac_dnase_example

Session Information 

utils::sessionInfo()
## R version 4.4.0 RC (2024-04-16 r86441)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.31.0
## 
## loaded via a namespace (and not attached):
##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.46         
##  [4] rlang_1.1.3         xfun_0.43           purrr_1.0.2        
##  [7] textshaping_0.3.7   jsonlite_1.8.8      htmltools_0.5.8.1  
## [10] ragg_1.3.0          sass_0.4.9          rmarkdown_2.26     
## [13] evaluate_0.23       jquerylib_0.1.4     fastmap_1.1.1      
## [16] yaml_2.3.8          lifecycle_1.0.4     memoise_2.0.1      
## [19] bookdown_0.39       BiocManager_1.30.22 compiler_4.4.0     
## [22] fs_1.6.4            htmlwidgets_1.6.4   systemfonts_1.0.6  
## [25] digest_0.6.35       R6_2.5.1            magrittr_2.0.3     
## [28] bslib_0.7.0         tools_4.4.0         pkgdown_2.0.9      
## [31] cachem_1.0.8        desc_1.4.3