Example report


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


Vignette updated: Oct-18-2024

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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 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_2.33.1
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       desc_1.4.3          R6_2.5.1           
##  [4] bookdown_0.41       fastmap_1.2.0       xfun_0.48          
##  [7] cachem_1.1.0        knitr_1.48          htmltools_0.5.8.1  
## [10] rmarkdown_2.28      lifecycle_1.0.4     cli_3.6.3          
## [13] sass_0.4.9          pkgdown_2.1.1       textshaping_0.4.0  
## [16] jquerylib_0.1.4     systemfonts_1.1.0   compiler_4.4.1     
## [19] tools_4.4.1         ragg_1.3.3          bslib_0.8.0        
## [22] evaluate_1.0.1      yaml_2.3.10         BiocManager_1.30.25
## [25] jsonlite_1.8.9      rlang_1.1.4         fs_1.6.4           
## [28] htmlwidgets_1.6.4