Abstract

Todo

Introduction

Todo

R session information

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R-3.6.0.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R-3.6.0.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] datasets  utils     grDevices graphics  stats     methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.12.0
## 
## loaded via a namespace (and not attached):
##   [1] ProtGenerics_1.16.0           bitops_1.0-6                 
##   [3] matrixStats_0.54.0            fs_1.3.0                     
##   [5] bit64_0.9-7                   progress_1.2.0               
##   [7] RColorBrewer_1.1-2            httr_1.4.0                   
##   [9] rprojroot_1.3-2               GenomeInfoDb_1.20.0          
##  [11] UpSetR_1.3.3                  syntactic_0.1.9              
##  [13] acidplots_0.2.3               tools_3.6.0                  
##  [15] backports_1.1.4               R6_2.4.0                     
##  [17] DBI_1.0.0                     lazyeval_0.2.2               
##  [19] BiocGenerics_0.30.0           colorspace_1.4-1             
##  [21] withr_2.1.2                   prettyunits_1.0.2            
##  [23] tidyselect_0.2.5              gridExtra_2.3                
##  [25] bit_1.1-14                    curl_3.3                     
##  [27] compiler_3.6.0                cli_1.1.0                    
##  [29] basejump_0.10.8               Biobase_2.44.0               
##  [31] xml2_1.2.0                    desc_1.2.0                   
##  [33] DelayedArray_0.10.0           rtracklayer_1.44.0           
##  [35] bookdown_0.9                  scales_1.0.0                 
##  [37] readr_1.3.1                   rappdirs_0.3.1               
##  [39] pkgdown_1.3.0.9000            commonmark_1.7               
##  [41] stringr_1.4.0                 digest_0.6.18                
##  [43] Rsamtools_2.0.0               rmarkdown_1.12               
##  [45] R.utils_2.8.0                 XVector_0.24.0               
##  [47] pkgconfig_2.0.2               htmltools_0.3.6              
##  [49] sessioninfo_1.1.1             ensembldb_2.8.0              
##  [51] dbplyr_1.4.0                  rlang_0.3.4                  
##  [53] RSQLite_2.1.1                 shiny_1.3.2                  
##  [55] BiocParallel_1.18.0           dplyr_0.8.0.1                
##  [57] R.oo_1.22.0                   RCurl_1.95-4.12              
##  [59] magrittr_1.5                  GenomeInfoDbData_1.2.1       
##  [61] Matrix_1.2-17                 Rcpp_1.0.1                   
##  [63] munsell_0.5.0                 S4Vectors_0.22.0             
##  [65] R.methodsS3_1.7.1             stringi_1.4.3                
##  [67] yaml_2.2.0                    MASS_7.3-51.4                
##  [69] SummarizedExperiment_1.14.0   zlibbioc_1.30.0              
##  [71] brio_0.2.0                    goalie_0.2.16                
##  [73] plyr_1.8.4                    BiocFileCache_1.8.0          
##  [75] AnnotationHub_2.16.0          grid_3.6.0                   
##  [77] blob_1.1.1                    ggrepel_0.8.0                
##  [79] promises_1.0.1                parallel_3.6.0               
##  [81] transformer_0.1.11            crayon_1.3.4                 
##  [83] lattice_0.20-38               cowplot_0.9.4                
##  [85] Biostrings_2.52.0             bioverbs_0.1.18              
##  [87] GenomicFeatures_1.36.0        hms_0.4.2                    
##  [89] knitr_1.22                    pillar_1.3.1                 
##  [91] GenomicRanges_1.36.0          reshape2_1.4.3               
##  [93] biomaRt_2.40.0                stats4_3.6.0                 
##  [95] XML_3.98-1.19                 glue_1.3.1                   
##  [97] evaluate_0.13                 freerange_0.1.6              
##  [99] data.table_1.12.2             BiocManager_1.30.4           
## [101] httpuv_1.5.1                  tidyr_0.8.3                  
## [103] gtable_0.3.0                  grr_0.9.5                    
## [105] purrr_0.3.2                   assertthat_0.2.1             
## [107] ggplot2_3.1.1                 xfun_0.6                     
## [109] mime_0.6                      xtable_1.8-4                 
## [111] AnnotationFilter_1.8.0        later_0.8.0                  
## [113] roxygen2_6.1.1                pheatmap_1.0.12              
## [115] SingleCellExperiment_1.6.0    tibble_2.1.1                 
## [117] AnnotationDbi_1.46.0          GenomicAlignments_1.20.0     
## [119] Matrix.utils_0.9.7            memoise_1.1.0                
## [121] IRanges_2.18.0                interactiveDisplayBase_1.22.0

References

The papers and software cited in our workflows are available as a shared library on Paperpile.