Last updated: 2018-09-25

Code version: f9c0f68

First we need to import normalized RNA-seq and microarray data:

Session Information

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Gentoo/Linux

Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] BSgenome.Pfalciparum.PlasmoDB.v24_1.0
 [2] BSgenome_1.48.0                      
 [3] rtracklayer_1.40.6                   
 [4] Biostrings_2.48.0                    
 [5] XVector_0.20.0                       
 [6] GenomicRanges_1.32.6                 
 [7] GenomeInfoDb_1.16.0                  
 [8] org.Pf.plasmo.db_3.6.0               
 [9] AnnotationDbi_1.42.1                 
[10] IRanges_2.14.10                      
[11] S4Vectors_0.18.3                     
[12] Biobase_2.40.0                       
[13] BiocGenerics_0.26.0                  
[14] scales_1.0.0                         
[15] cowplot_0.9.3                        
[16] magrittr_1.5                         
[17] forcats_0.3.0                        
[18] stringr_1.3.1                        
[19] dplyr_0.7.6                          
[20] purrr_0.2.5                          
[21] readr_1.1.1                          
[22] tidyr_0.8.1                          
[23] tibble_1.4.2                         
[24] ggplot2_3.0.0                        
[25] tidyverse_1.2.1                      

loaded via a namespace (and not attached):
 [1] nlme_3.1-137                bitops_1.0-6               
 [3] matrixStats_0.54.0          lubridate_1.7.4            
 [5] bit64_0.9-7                 httr_1.3.1                 
 [7] rprojroot_1.3-2             tools_3.5.0                
 [9] backports_1.1.2             utf8_1.1.4                 
[11] R6_2.2.2                    DBI_1.0.0                  
[13] lazyeval_0.2.1              colorspace_1.3-2           
[15] withr_2.1.2                 tidyselect_0.2.4           
[17] bit_1.1-14                  compiler_3.5.0             
[19] git2r_0.23.0                cli_1.0.0                  
[21] rvest_0.3.2                 xml2_1.2.0                 
[23] DelayedArray_0.6.5          labeling_0.3               
[25] digest_0.6.15               Rsamtools_1.32.3           
[27] rmarkdown_1.10              R.utils_2.6.0              
[29] pkgconfig_2.0.2             htmltools_0.3.6            
[31] rlang_0.2.2                 readxl_1.1.0               
[33] rstudioapi_0.7              RSQLite_2.1.1              
[35] bindr_0.1.1                 jsonlite_1.5               
[37] BiocParallel_1.14.2         R.oo_1.22.0                
[39] RCurl_1.95-4.11             GenomeInfoDbData_1.1.0     
[41] Matrix_1.2-14               fansi_0.3.0                
[43] Rcpp_0.12.18                munsell_0.5.0              
[45] R.methodsS3_1.7.1           stringi_1.2.4              
[47] yaml_2.2.0                  SummarizedExperiment_1.10.1
[49] zlibbioc_1.26.0             plyr_1.8.4                 
[51] grid_3.5.0                  blob_1.1.1                 
[53] crayon_1.3.4                lattice_0.20-35            
[55] haven_1.1.2                 hms_0.4.2                  
[57] knitr_1.20                  pillar_1.3.0               
[59] reshape2_1.4.3              XML_3.98-1.16              
[61] glue_1.3.0                  evaluate_0.11              
[63] modelr_0.1.2                cellranger_1.1.0           
[65] gtable_0.2.0                assertthat_0.2.0           
[67] broom_0.5.0                 ggcorrplot_0.1.2           
[69] GenomicAlignments_1.16.0    memoise_1.1.0              
[71] workflowr_1.1.1             bindrcpp_0.2.2

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