Unfiltered/raw data

Counts CDF

Histogram of cpm values by sample

Sample Correlation heatmap (unfiltered data)

Variance within replicates

Plasmid expression (log 2 cpm values for Day 0 sample/time point)

Applying potential filters

Filter pgRNAs where there is a count of 0 for any sample/time point

Replicates with a pgRNA count of 0

If this filter is applied, this is the number of pgRNAs that would be filtered out

RawCount0 n percent
FALSE 31978 96.41
TRUE 1192 3.59

Filter pgRNAs where there is a low log2 CPM value for the plasmid sample/time point

If this filter is applied, this is the number of pgRNAs that would be filtered out

Plasmid_log2cpmBelowCutoff n percent
FALSE 32873 99.1
TRUE 297 0.9

If both filters are applied

Which Filter(s) Number of pgRNAs flagged for removal Percent of total pgRNA constructs
Zero count, but not low plasmid CPM 1056 3.18
Low plasmid CPM, but not zero count 161 0.49
Either Zero count or Low plasmid CPM or both 1353 4.08
Both Zero count and Low plasmid CPM 136 0.41
Remaining pgRNAs flagged by no filters 31817 95.92

Session Info

## R version 4.5.0 (2025-04-11)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sequoia 15.4.1
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods  
## [7] base     
## 
## other attached packages:
## [1] purrr_1.0.4    ggplot2_3.5.2  gimap_1.1.1    testthat_3.2.3
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6       bslib_0.9.0        xfun_0.52         
##  [4] htmlwidgets_1.6.4  devtools_2.4.5     remotes_2.5.0     
##  [7] processx_3.8.6     tzdb_0.5.0         callr_3.7.6       
## [10] vctrs_0.6.5        tools_4.5.0        ps_1.9.1          
## [13] generics_0.1.4     parallel_4.5.0     curl_6.2.2        
## [16] tibble_3.2.1       pkgconfig_2.0.3    pheatmap_1.0.13   
## [19] RColorBrewer_1.1-3 desc_1.4.3         lifecycle_1.0.4   
## [22] compiler_4.5.0     farver_2.1.2       stringr_1.5.1     
## [25] brio_1.1.5         janitor_2.2.1      snakecase_0.11.1  
## [28] httpuv_1.6.16      sass_0.4.10        htmltools_0.5.8.1 
## [31] usethis_3.1.0      yaml_2.3.10        jquerylib_0.1.4   
## [34] crayon_1.5.3       later_1.4.2        pillar_1.10.2     
## [37] urlchecker_1.0.1   tidyr_1.3.1        ellipsis_0.3.2    
## [40] openssl_2.3.2      cachem_1.1.0       sessioninfo_1.2.3 
## [43] mime_0.13          tidyselect_1.2.1   digest_0.6.37     
## [46] stringi_1.8.7      dplyr_1.1.4        labeling_0.4.3    
## [49] rprojroot_2.0.4    fastmap_1.2.0      grid_4.5.0        
## [52] cli_3.6.5          magrittr_2.0.3     pkgbuild_1.4.7    
## [55] readr_2.1.5        withr_3.0.2        scales_1.4.0      
## [58] promises_1.3.2     bit64_4.6.0-1      lubridate_1.9.4   
## [61] timechange_0.3.0   rmarkdown_2.29     httr_1.4.7        
## [64] bit_4.6.0          askpass_1.2.1      hms_1.1.3         
## [67] memoise_2.0.1      shiny_1.10.0       evaluate_1.0.3    
## [70] knitr_1.50         miniUI_0.1.2       profvis_0.4.0     
## [73] rlang_1.1.6        Rcpp_1.0.14        xtable_1.8-4      
## [76] glue_1.8.0         pkgload_1.4.0      vroom_1.6.5       
## [79] rstudioapi_0.17.1  jsonlite_2.0.0     R6_2.6.1          
## [82] fs_1.6.6