Repository for the preprint "Identifying cell-to-cell variability in internalisation using flow cytometry" available on bioRxiv.
All data used in the analysis is available in Data. Due to GitHub size limitations, the script ProcessData.jl must be run to process individual gated .fcs files into a CSV file used for analysis.
Code to produce all results is contained within this repository, including the Julia modules Inference and Model. To download, first clone this Github repo. Next, add the two module folders to your LOAD_PATH:
push!(LOAD_PATH,"/path/to/repo/Module/Inference")
push!(LOAD_PATH,"/path/to/repo/Module/Model")
Next, run the following code (press ] to enter the Pkg REPL) to install all required packages and activate the project
(v1.6) pkg> activate .
(Spheroids) pkg> instantiate
Scripts to produce the results are available in the Results folder. For example, to produce the main results, run MainResult_Inference.jl (takes approximately 24 h to perform ABC on a standard, quad-core machine). For convenience, this script saves its output to MainResult.jld2.
Code used to produce each figure in the main document and supplementary material is available in the Figures folder. For example, to reproduce Figure 4, run Figures/Fig4/Fig4.jl.