Note: the most recent version of this tutorial can be found here.

sessionInfo()
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04 LTS
## 
## Matrix products: default
## BLAS:   /usr/local/bin/R/lib/R/lib/libRblas.so
## LAPACK: /usr/local/bin/R/lib/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] DESeq2_1.28.0               magrittr_1.5               
##  [3] batchtools_0.9.13           ape_5.3                    
##  [5] ggplot2_3.3.0               systemPipeR_1.23.0         
##  [7] ShortRead_1.46.0            GenomicAlignments_1.24.0   
##  [9] SummarizedExperiment_1.18.1 DelayedArray_0.14.0        
## [11] matrixStats_0.56.0          Biobase_2.48.0             
## [13] BiocParallel_1.22.0         Rsamtools_2.4.0            
## [15] Biostrings_2.56.0           XVector_0.28.0             
## [17] GenomicRanges_1.40.0        GenomeInfoDb_1.24.0        
## [19] IRanges_2.22.1              S4Vectors_0.26.0           
## [21] BiocGenerics_0.34.0         BiocStyle_2.16.0           
## 
## loaded via a namespace (and not attached):
##   [1] colorspace_1.4-1         rjson_0.2.20             hwriter_1.3.2           
##   [4] ellipsis_0.3.0           farver_2.0.3             bit64_0.9-7             
##   [7] AnnotationDbi_1.50.0     codetools_0.2-16         splines_4.0.0           
##  [10] geneplotter_1.66.0       knitr_1.28               jsonlite_1.6.1          
##  [13] annotate_1.66.0          GO.db_3.11.0             dbplyr_1.4.3            
##  [16] png_0.1-7                pheatmap_1.0.12          graph_1.66.0            
##  [19] BiocManager_1.30.10      compiler_4.0.0           httr_1.4.1              
##  [22] GOstats_2.54.0           backports_1.1.6          assertthat_0.2.1        
##  [25] Matrix_1.2-18            limma_3.44.1             formatR_1.7             
##  [28] htmltools_0.4.0          prettyunits_1.1.1        tools_4.0.0             
##  [31] gtable_0.3.0             glue_1.4.0               GenomeInfoDbData_1.2.3  
##  [34] Category_2.54.0          dplyr_0.8.5              rsvg_1.3                
##  [37] rappdirs_0.3.1           V8_3.0.2                 Rcpp_1.0.4.6            
##  [40] vctrs_0.2.4              nlme_3.1-147             rtracklayer_1.48.0      
##  [43] xfun_0.13                stringr_1.4.0            lifecycle_0.2.0         
##  [46] XML_3.99-0.3             edgeR_3.30.0             zlibbioc_1.34.0         
##  [49] scales_1.1.0             BSgenome_1.56.0          VariantAnnotation_1.34.0
##  [52] hms_0.5.3                RBGL_1.64.0              RColorBrewer_1.1-2      
##  [55] yaml_2.2.1               curl_4.3                 memoise_1.1.0           
##  [58] biomaRt_2.44.0           latticeExtra_0.6-29      stringi_1.4.6           
##  [61] RSQLite_2.2.0            genefilter_1.70.0        checkmate_2.0.0         
##  [64] GenomicFeatures_1.40.0   DOT_0.1                  rlang_0.4.6             
##  [67] pkgconfig_2.0.3          bitops_1.0-6             evaluate_0.14           
##  [70] lattice_0.20-41          purrr_0.3.4              labeling_0.3            
##  [73] bit_1.1-15.2             tidyselect_1.0.0         GSEABase_1.50.0         
##  [76] AnnotationForge_1.30.1   bookdown_0.18            R6_2.4.1                
##  [79] base64url_1.4            DBI_1.1.0                pillar_1.4.3            
##  [82] withr_2.2.0              survival_3.1-12          RCurl_1.98-1.2          
##  [85] tibble_3.0.1             crayon_1.3.4             BiocFileCache_1.12.0    
##  [88] rmarkdown_2.1            jpeg_0.1-8.1             progress_1.2.2          
##  [91] locfit_1.5-9.4           grid_4.0.0               data.table_1.12.8       
##  [94] blob_1.2.1               Rgraphviz_2.32.0         digest_0.6.25           
##  [97] xtable_1.8-4             brew_1.0-6               openssl_1.4.1           
## [100] munsell_0.5.0            askpass_1.1



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