oneiric

Simulated Spatial Transcriptomic data.

o·nei·ric (/ōˈnīrik/): relating to dreams or dreaming.

Why a package?

Simulation are an essential tool kit to benchmark computational methods. Here, we developped a simple package that convenietly wraps the code we used to generate our simulated data.

We hope that this approach will improve reproducibility and replicability of our results.

We created and tested our simulations on the following OS:

• macOS sequoia 15.0
• Red Hat Enterprise Linux 8.5 (Ootpa)

Installation

From GitHub

library(devtools)
install_github("WonLab-CS/oneiric")

From source

First, clone the repository. Alternatively, you can download the zip file and unpack the repository.

git clone https://github.com/WonLab-CS/oneiric.git
cd oneiric 

Then from the command line

R CMD build oneiric
Rscript -e "install.packages("oneiric_0.0.1.tar.gz, repos  = NULL)

Generating Simulations

We provide a vignette showing different options to generate simulate data.

If you only wish to generate the data sets used in the Vesalius pre-print, you can use the following:

library(ggplot2)
library(RColorBrewer)
library(oneric)

# USE THIS SEED TO REPRODUCE THE DATA SETS USED IN PAPER
output <- "/path/to/output/"
seed <- 1453

generate_sim_data(output = output,
    seed = seed,
    plot = TRUE,
    run_mem = TRUE,
    simple = TRUE)

Gen AI Disclaimer

Manual pages were refined/generated using Grok Code. Unit tests were generated using Grok Code.