Last updated: 2018-10-01

Code version: b1b8980

Using the cageR software package, we were able to detect around 70 genes with “shifting promoters.” We define this as a shift of at least 100 base pairs in a gene’s primary TSS between two points throughout the P. falciparum blood stage.

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  100.0   158.2   206.5   231.0   272.2   772.0 

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] bindrcpp_0.2.2                       
 [2] BSgenome.Pfalciparum.PlasmoDB.v24_1.0
 [3] BSgenome_1.48.0                      
 [4] rtracklayer_1.40.6                   
 [5] Biostrings_2.48.0                    
 [6] XVector_0.20.0                       
 [7] GenomicRanges_1.32.6                 
 [8] GenomeInfoDb_1.16.0                  
 [9] org.Pf.plasmo.db_3.6.0               
[10] AnnotationDbi_1.42.1                 
[11] IRanges_2.14.10                      
[12] S4Vectors_0.18.3                     
[13] Biobase_2.40.0                       
[14] BiocGenerics_0.26.0                  
[15] scales_1.0.0                         
[16] cowplot_0.9.3                        
[17] magrittr_1.5                         
[18] forcats_0.3.0                        
[19] stringr_1.3.1                        
[20] dplyr_0.7.6                          
[21] purrr_0.2.5                          
[22] readr_1.1.1                          
[23] tidyr_0.8.1                          
[24] tibble_1.4.2                         
[25] ggplot2_3.0.0                        
[26] 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             R6_2.2.2                   
[11] DBI_1.0.0                   lazyeval_0.2.1             
[13] colorspace_1.3-2            withr_2.1.2                
[15] tidyselect_0.2.4            bit_1.1-14                 
[17] compiler_3.5.0              git2r_0.23.0               
[19] cli_1.0.0                   rvest_0.3.2                
[21] xml2_1.2.0                  DelayedArray_0.6.5         
[23] labeling_0.3                digest_0.6.15              
[25] Rsamtools_1.32.3            rmarkdown_1.10             
[27] R.utils_2.6.0               pkgconfig_2.0.2            
[29] htmltools_0.3.6             rlang_0.2.2                
[31] readxl_1.1.0                rstudioapi_0.7             
[33] RSQLite_2.1.1               bindr_0.1.1                
[35] jsonlite_1.5                BiocParallel_1.14.2        
[37] R.oo_1.22.0                 RCurl_1.95-4.11            
[39] GenomeInfoDbData_1.1.0      Matrix_1.2-14              
[41] Rcpp_0.12.18                munsell_0.5.0              
[43] R.methodsS3_1.7.1           stringi_1.2.4              
[45] yaml_2.2.0                  SummarizedExperiment_1.10.1
[47] zlibbioc_1.26.0             plyr_1.8.4                 
[49] grid_3.5.0                  blob_1.1.1                 
[51] crayon_1.3.4                lattice_0.20-35            
[53] haven_1.1.2                 hms_0.4.2                  
[55] knitr_1.20                  pillar_1.3.0               
[57] XML_3.98-1.16               glue_1.3.0                 
[59] evaluate_0.11               modelr_0.1.2               
[61] cellranger_1.1.0            gtable_0.2.0               
[63] assertthat_0.2.0            broom_0.5.0                
[65] GenomicAlignments_1.16.0    memoise_1.1.0              
[67] workflowr_1.1.1            

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