For the sake of reproducibility, here’s a list of packages and their versions that were used to create this R markdown document.

devtools::session_info()
 setting  value                       
 version  R version 3.3.2 (2016-10-31)
 system   x86_64, darwin13.4.0        
 ui       RStudio (1.0.136)           
 language (EN)                        
 collate  en_CA.UTF-8                 
 tz       America/Vancouver           
 date     2017-03-27                  

 package                     * version    date       source                              
 acepack                       1.4.1      2016-10-29 CRAN (R 3.3.0)                      
 affy                          1.52.0     2016-10-18 Bioconductor                        
 affyio                        1.44.0     2016-10-18 Bioconductor                        
 annotate                      1.52.1     2016-12-22 Bioconductor                        
 AnnotationDbi                 1.36.2     2017-01-30 Bioconductor                        
 assertthat                    0.1        2013-12-06 CRAN (R 3.3.0)                      
 backports                     1.0.5      2017-01-18 CRAN (R 3.3.2)                      
 base64enc                     0.1-3      2015-07-28 CRAN (R 3.3.0)                      
 Biobase                     * 2.34.0     2016-10-18 Bioconductor                        
 BiocGenerics                * 0.20.0     2016-10-18 Bioconductor                        
 BiocInstaller                 1.24.0     2016-10-18 Bioconductor                        
 BiocParallel                  1.8.1      2016-10-30 Bioconductor                        
 biomaRt                     * 2.30.0     2016-10-18 Bioconductor                        
 Biostrings                    2.42.1     2016-12-01 Bioconductor                        
 bitops                        1.0-6      2013-08-17 CRAN (R 3.3.0)                      
 broom                         0.4.2      2017-02-13 CRAN (R 3.3.2)                      
 BSgenome                      1.42.0     2016-10-18 Bioconductor                        
 BSgenome.Hsapiens.UCSC.hg38   1.4.1      2017-03-08 Bioconductor                        
 changepoint                   2.2.2      2016-10-04 CRAN (R 3.3.0)                      
 checkmate                     1.8.2      2016-11-02 CRAN (R 3.3.0)                      
 circlize                      0.3.10     2017-03-07 CRAN (R 3.3.2)                      
 class                         7.3-14     2015-08-30 CRAN (R 3.3.2)                      
 cluster                     * 2.0.5      2016-10-08 CRAN (R 3.3.2)                      
 codetools                     0.2-15     2016-10-05 CRAN (R 3.3.2)                      
 colorspace                    1.3-2      2016-12-14 CRAN (R 3.3.2)                      
 cometExactTest                0.1.3      2015-10-31 CRAN (R 3.3.0)                      
 ComplexHeatmap                1.12.0     2016-10-14 Bioconductor (R 3.3.1)              
 corrplot                      0.77       2016-04-21 CRAN (R 3.3.0)                      
 cowplot                       0.7.0      2016-10-28 CRAN (R 3.3.0)                      
 crayon                        1.3.2      2016-06-28 CRAN (R 3.3.0)                      
 data.table                  * 1.10.4     2017-02-01 CRAN (R 3.3.0)                      
 DBI                           0.6        2017-03-09 CRAN (R 3.3.2)                      
 dendextend                    1.4.0      2017-01-21 cran (@1.4.0)                       
 DEoptimR                      1.0-8      2016-11-19 cran (@1.0-8)                       
 DESeq2                      * 1.14.1     2016-12-01 Bioconductor                        
 devtools                      1.12.0     2016-06-24 CRAN (R 3.3.0)                      
 digest                        0.6.12     2017-01-27 CRAN (R 3.3.2)                      
 diptest                       0.75-7     2015-06-08 cran (@0.75-7)                      
 doMC                          1.3.4      2015-10-13 CRAN (R 3.3.0)                      
 doParallel                    1.0.10     2015-10-14 CRAN (R 3.3.0)                      
 dplyr                       * 0.5.0      2016-06-24 CRAN (R 3.3.0)                      
 DPpackage                     1.1-6      2012-09-14 CRAN (R 3.3.0)                      
 evaluate                      0.10       2016-10-11 CRAN (R 3.3.0)                      
 FField                        0.1.0      2013-06-28 CRAN (R 3.3.0)                      
 flexmix                       2.3-13     2015-01-17 cran (@2.3-13)                      
 forcats                     * 0.2.0      2017-01-23 CRAN (R 3.3.2)                      
 foreach                       1.4.3      2015-10-13 CRAN (R 3.3.0)                      
 foreign                       0.8-67     2016-09-13 CRAN (R 3.3.2)                      
 Formula                       1.2-1      2015-04-07 CRAN (R 3.3.0)                      
 fpc                           2.1-10     2015-08-14 cran (@2.1-10)                      
 genefilter                    1.56.0     2016-10-18 Bioconductor                        
 geneplotter                   1.52.0     2016-10-18 Bioconductor                        
 GenomeInfoDb                * 1.10.3     2017-02-07 Bioconductor                        
 GenomicAlignments             1.10.0     2016-10-18 Bioconductor                        
 GenomicFeatures               1.26.3     2017-02-22 Bioconductor                        
 GenomicRanges               * 1.26.3     2017-02-25 Bioconductor                        
 GenVisR                       1.4.7      2017-03-09 Github (griffithlab/GenVisR@974177f)
 GetoptLong                    0.1.6      2017-03-07 CRAN (R 3.3.2)                      
 ggplot2                     * 2.2.1      2016-12-30 CRAN (R 3.3.2)                      
 ggrepel                       0.6.5      2016-11-24 CRAN (R 3.3.2)                      
 GlobalOptions                 0.0.11     2017-03-06 CRAN (R 3.3.2)                      
 gridBase                      0.4-7      2014-02-24 CRAN (R 3.3.0)                      
 gridExtra                     2.2.1      2016-02-29 CRAN (R 3.3.0)                      
 gtable                        0.2.0      2016-02-26 CRAN (R 3.3.0)                      
 gtools                        3.5.0      2015-05-29 CRAN (R 3.3.0)                      
 haven                         1.0.0      2016-09-23 CRAN (R 3.3.0)                      
 hexbin                      * 1.27.1     2015-08-19 CRAN (R 3.3.0)                      
 Hmisc                         4.0-2      2016-12-31 CRAN (R 3.3.2)                      
 hms                           0.3        2016-11-22 CRAN (R 3.3.2)                      
 htmlTable                     1.9        2017-01-26 CRAN (R 3.3.2)                      
 htmltools                     0.3.5      2016-03-21 CRAN (R 3.3.0)                      
 htmlwidgets                   0.8        2016-11-09 CRAN (R 3.3.2)                      
 httr                          1.2.1      2016-07-03 CRAN (R 3.3.0)                      
 IRanges                     * 2.8.1      2016-11-08 Bioconductor                        
 iterators                     1.0.8      2015-10-13 CRAN (R 3.3.0)                      
 jsonlite                      1.3        2017-02-28 CRAN (R 3.3.2)                      
 kernlab                       0.9-25     2016-10-03 cran (@0.9-25)                      
 knitr                         1.15.1     2016-11-22 CRAN (R 3.3.2)                      
 labeling                      0.3        2014-08-23 CRAN (R 3.3.0)                      
 lattice                       0.20-34    2016-09-06 CRAN (R 3.3.2)                      
 latticeExtra                  0.6-28     2016-02-09 CRAN (R 3.3.0)                      
 lazyeval                      0.2.0      2016-06-12 CRAN (R 3.3.0)                      
 limma                         3.30.12    2017-03-05 Bioconductor                        
 locfit                        1.5-9.1    2013-04-20 CRAN (R 3.3.0)                      
 lubridate                     1.6.0      2016-09-13 CRAN (R 3.3.0)                      
 maftools                    * 1.0.50     2017-02-23 Bioconductor                        
 magrittr                    * 1.5        2014-11-22 CRAN (R 3.3.0)                      
 MASS                          7.3-45     2016-04-21 CRAN (R 3.3.2)                      
 Matrix                        1.2-8      2017-01-20 CRAN (R 3.3.2)                      
 matrixStats                 * 0.51.0     2016-10-09 CRAN (R 3.3.0)                      
 mclust                        5.2.2      2017-01-22 cran (@5.2.2)                       
 memoise                       1.0.0      2016-01-29 CRAN (R 3.3.0)                      
 mgcv                          1.8-17     2017-02-08 CRAN (R 3.3.2)                      
 mnormt                        1.5-5      2016-10-15 CRAN (R 3.3.0)                      
 modelr                        0.1.0      2016-08-31 CRAN (R 3.3.0)                      
 modeltools                    0.2-21     2013-09-02 cran (@0.2-21)                      
 munsell                       0.4.3      2016-02-13 CRAN (R 3.3.0)                      
 mvtnorm                       1.0-6      2017-03-02 CRAN (R 3.3.2)                      
 nlme                          3.1-131    2017-02-06 CRAN (R 3.3.2)                      
 NMF                         * 0.20.6     2015-05-26 CRAN (R 3.3.0)                      
 nnet                          7.3-12     2016-02-02 CRAN (R 3.3.2)                      
 pheatmap                      1.0.8      2015-12-11 CRAN (R 3.3.0)                      
 pkgmaker                    * 0.22       2014-05-14 CRAN (R 3.3.0)                      
 plyr                          1.8.4      2016-06-08 CRAN (R 3.3.0)                      
 prabclus                      2.2-6      2015-01-14 cran (@2.2-6)                       
 preprocessCore                1.36.0     2016-10-18 Bioconductor                        
 psych                         1.6.12     2017-01-08 CRAN (R 3.3.2)                      
 purrr                       * 0.2.2      2016-06-18 CRAN (R 3.3.0)                      
 R6                            2.2.0      2016-10-05 CRAN (R 3.3.0)                      
 RColorBrewer                  1.1-2      2014-12-07 CRAN (R 3.3.0)                      
 Rcpp                          0.12.10    2017-03-19 cran (@0.12.10)                     
 RCurl                         1.95-4.8   2016-03-01 CRAN (R 3.3.0)                      
 readr                       * 1.0.0      2016-08-03 CRAN (R 3.3.0)                      
 readxl                        0.1.1.9000 2017-02-22 Github (tidyverse/readxl@3338f92)   
 registry                    * 0.3        2015-07-08 CRAN (R 3.3.0)                      
 reshape2                      1.4.2      2016-10-22 CRAN (R 3.3.0)                      
 rjson                         0.2.15     2014-11-03 CRAN (R 3.3.0)                      
 rmarkdown                   * 1.3        2016-12-21 CRAN (R 3.3.2)                      
 rngtools                    * 1.2.4      2014-03-06 CRAN (R 3.3.0)                      
 robustbase                    0.92-7     2016-12-09 cran (@0.92-7)                      
 rpart                         4.1-10     2015-06-29 CRAN (R 3.3.2)                      
 rprojroot                     1.2        2017-01-16 CRAN (R 3.3.2)                      
 Rsamtools                     1.26.1     2016-10-22 Bioconductor                        
 RSQLite                       1.1-2      2017-01-08 CRAN (R 3.3.2)                      
 rtracklayer                   1.34.2     2017-02-19 Bioconductor                        
 rvest                         0.3.2      2016-06-17 CRAN (R 3.3.0)                      
 S4Vectors                   * 0.12.1     2016-12-01 Bioconductor                        
 scales                        0.4.1      2016-11-09 CRAN (R 3.3.2)                      
 shape                         1.4.2      2014-11-05 CRAN (R 3.3.0)                      
 slam                          0.1-40     2016-12-01 CRAN (R 3.3.2)                      
 stringi                       1.1.2      2016-10-01 CRAN (R 3.3.0)                      
 stringr                       1.2.0      2017-02-18 CRAN (R 3.3.2)                      
 SummarizedExperiment        * 1.4.0      2016-10-18 Bioconductor                        
 survival                      2.40-1     2016-10-30 CRAN (R 3.3.0)                      
 sva                           3.22.0     2016-10-18 Bioconductor                        
 testthat                      1.0.2      2016-04-23 CRAN (R 3.3.0)                      
 tibble                      * 1.2        2016-08-26 CRAN (R 3.3.0)                      
 tidyr                       * 0.6.1      2017-01-10 CRAN (R 3.3.2)                      
 tidyverse                   * 1.1.1      2017-01-27 CRAN (R 3.3.2)                      
 trimcluster                   0.1-2      2012-10-29 cran (@0.1-2)                       
 VariantAnnotation             1.20.2     2016-12-01 Bioconductor                        
 viridis                       0.3.4      2016-03-12 CRAN (R 3.3.0)                      
 vsn                           3.42.3     2016-10-24 Bioconductor                        
 whisker                       0.3-2      2013-04-28 CRAN (R 3.3.0)                      
 withr                         1.0.2      2016-06-20 CRAN (R 3.3.0)                      
 wordcloud                     2.5        2014-06-13 CRAN (R 3.3.0)                      
 XML                           3.98-1.5   2016-11-10 CRAN (R 3.3.2)                      
 xml2                          1.1.1      2017-01-24 CRAN (R 3.3.2)                      
 xtable                        1.8-2      2016-02-05 CRAN (R 3.3.0)                      
 XVector                       0.14.0     2016-10-18 Bioconductor                        
 yaml                          2.1.14     2016-11-12 CRAN (R 3.3.2)                      
 zlibbioc                      1.20.0     2016-10-18 Bioconductor                        
 zoo                           1.7-14     2016-12-16 CRAN (R 3.3.2)