Toolbox for organoids analyses using drug screening and RNA-sequencing

Package: OrganoidsToolBox
Authors: Pascal Belleau [aut] (https://orcid.org/0000-0002-0802-1071), Astrid Deschênes [cre, aut] (https://orcid.org/0000-0001-7846-6749), Amber Habowski [dtc], David A. Tuveson [fnd] (https://orcid.org/0000-0002-8017-2712), Alexander Krasnitz [fnd, aut]
Version: 0.0.1
Compiled date: 2022-10-25
License: Artistic-2.0

Licensing

The OrganoidsToolBox package and the underlying OrganoidsToolBox code are distributed under
the Artistic-2.0 license. You are free to use and redistribute this software.

Citing

If you use the OrganoidsToolBox package for a publication, we would ask you to cite the following:

TODO

Introduction

TODO

Installation

To install the latest version accessible on the OrganoidsToolBox Github Website, the devtools package is required.

## Load required package
library(devtools)

## Install the latest version of OrganoidsToolBox
devtools::install_github('KrasnitzLab/OrganoidsToolBox')

Main Steps

Input

## Load drug screen dataset for 1 drug
data(drugScreening)

head(drugScreening)

##   Column1 organoid_id  plate passage_number timestamp     study screen_type
## 1       1      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
## 2       2      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
## 3       3      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
## 4       4      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
## 5       5      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
## 6       1      hT1001 Plate1            P16  2/2/1988 MEGA-TEST     TEST-01
##     z_prime       drug_a drug_b drug_c drug_background dosage_type
## 1 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
## 2 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
## 3 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
## 4 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
## 5 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
## 6 0.2732018 Methotrexate    N/A    N/A             N/A    Averaged
##   dosage_concentration_a dosage_concentration_b dosage_concentration_c
## 1             -2.1481304                      0                      0
## 2             -1.8477117                      0                      0
## 3             -1.3027707                      0                      0
## 4             -0.7495800                      0                      0
## 5             -0.1481304                      0                      0
## 6              0.3961993                      0                      0
##   dosage_concentration_background percent_viability     ic50      auc
## 1                               0          81.64214 1.072243 218.0053
## 2                               0          89.92993 1.072243 218.0053
## 3                               0          75.73226 1.072243 218.0053
## 4                               0          57.93407 1.072243 218.0053
## 5                               0          71.17445 1.072243 218.0053
## 6                               0          43.70780 1.072243 218.0053
##   relative_auc
## 1     52.61044
## 2     52.61044
## 3     52.61044
## 4     52.61044
## 5     52.61044
## 6     52.61044

Visualisation

## Load drug screen dataset for 1 drug
data(drugScreening)

## Calculate the extreme organoids for the methotrexate drug screening
## using a quantile of 1/3
results <- getClassOneDrug(drugScreening=drugScreening,
    drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
    doseType="Averaged", quantile=1/3)

## Create a density plot where drug sensitivity groups are split
densityGraph <- plotDrugAUCDensityCurve(results, byGroup=TRUE)
densityGraph

## Picking joint bandwidth of 3.58

Session info

Here is the output of sessionInfo() on the system on which this document was compiled:

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
## 
## 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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] OrganoidsToolBox_0.0.1 knitr_1.40             BiocStyle_2.24.0      
## 
## loaded via a namespace (and not attached):
##  [1] highr_0.9           pillar_1.8.1        bslib_0.4.0        
##  [4] compiler_4.2.1      BiocManager_1.30.18 jquerylib_0.1.4    
##  [7] tools_4.2.1         digest_0.6.30       tibble_3.1.8       
## [10] jsonlite_1.8.3      evaluate_0.17       memoise_2.0.1      
## [13] lifecycle_1.0.3     gtable_0.3.1        pkgconfig_2.0.3    
## [16] rlang_1.0.6         cli_3.4.1           yaml_2.3.6         
## [19] pkgdown_2.0.6       xfun_0.34           fastmap_1.1.0      
## [22] stringr_1.4.1       vctrs_0.5.0         desc_1.4.2         
## [25] fs_1.5.2            sass_0.4.2          S4Vectors_0.34.0   
## [28] systemfonts_1.0.4   stats4_4.2.1        rprojroot_2.0.3    
## [31] grid_4.2.1          glue_1.6.2          R6_2.5.1           
## [34] textshaping_0.3.6   fansi_1.0.3         rmarkdown_2.17     
## [37] bookdown_0.29       farver_2.1.1        purrr_0.3.5        
## [40] ggplot2_3.3.6       magrittr_2.0.3      ggridges_0.5.4     
## [43] scales_1.2.1        htmltools_0.5.3     BiocGenerics_0.42.0
## [46] colorspace_2.0-3    labeling_0.4.2      ragg_1.2.4         
## [49] utf8_1.2.2          stringi_1.7.8       munsell_0.5.0      
## [52] cachem_1.0.6

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz