This repository is made to host a reproducible version of the condiments paper. Some of the functions can take a long time to run and we have therefore saved intermediary objects. However, they can be entirely recreated by running all code blocks in the appropriate vignette.
You can access a preprint of the paper here and the condiments package is available on github here.
You can follow along the vignettes here.
There are 5 vignettes that follow along the paper
Examples
The first vignette is a list of all examples used in Figure 1 and S1 of the manuscript
Simulation
The second vignette contains the code to run all simulations. It is not run here but instead loads the data from this package to generate the plots from Figure 2, Figure S2-S5.
TGFB case study
The third vignette contains all the code to download the first dataset. It then loads the dataset from this package and conducts the analysis to generate Figures 3 and 4.
Fibrosis case study
The fourth vignette contains all the code to download the second dataset. It then loads the dataset from this package and conducts the analysis to generate Figures 5 and S6-7.
TCDD case study
The fifth vignette contains all the code to download the second dataset. It then loads the dataset from this package and conducts the analysis to generate Figures S8-9.
KRAS case study
The sixth and final vignette contains all the code to download the third dataset. It then loads the dataset from this package and conducts the analysis to generate Figures S10-12.