dyngen manuscript

dyngen is a multi-modal simulator for spearheading single-cell omics analyses. This repository contains all code necessary to reproduce the corresponding manuscript. For documentation of dyngen (examples, vignettes, instructions), visit the dyngen repository: https://github.com/dynverse/dyngen.

Install dependencies

Clone the repository as follows.

# clone the repo
git clone https://github.com/dynverse/dyngen_manuscript
cd dyngen_manuscript

Open the R project file inside Rstudio and run the following code.

# install the R package and its dependencies
devtools::install("package/", dependencies = TRUE)

Reproducing an analysis

For each separate experiment, the code to reproduce the analysis can be found in the analysis folder. Any output generated by those scripts will be stored in the results folder. Note that each of the scripts assume that the working directory is the dyngen_manuscript folder.

• analysis/usecase_network_inference: Evaluating the performance of cell-specific network inference algorithms.
• analysis/usecase_rna_velocity: Evaluating the performance of RNA velocity algorithms.
• analysis/usecase_trajectory_alignment: Evaluating the performance of trajectory algorithms.
• analysis/summary: Generate overview figures which summarise the aforementioned experiments.
• analysis/showcase_backbones: Generate visualisations for each of the predefined dyngen backbones.
• analysis/example_methods_overview: Small example for illustrating particular aspects in the methods section.

Build the manuscript

The complete manuscript (including supplementary files) can be built from the manuscript/render.Rmd file, which can by build by running the following code inside R.

library(rmarkdown)
render("manuscript/render.Rmd")