A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses
Backbone of the simulation model
List of all predefined backbone models
Design your own custom backbone easily
Combine multiple dyngen models
Convert simulation output to different formats.
dyngen: A multi-modal simulator for spearheading single-cell omics ana...
Simulate the cells
Generate a dataset
Sample cells from the simulations
Generate a target network
Simulate the gold standard
Determine the kinetics of the feature network
Generate a transcription factor network from the backbone
Return the timings of each of the dyngen steps
Initial settings for simulating a dyngen dataset
Add small noise to the kinetics of each simulation
Visualise the backbone of a model
Visualise the backbone state network of a model
Plot a dimensionality reduction of the final dataset
Visualise the feature network of a model
Visualise the expression of the gold standard over simulation time
Visualise the mapping of the simulations to the gold standard
Visualise the simulations using the dimred
Visualise the expression of the simulations over simulation time
Visualise the simulations using the dimred
Plot a summary of all dyngen simulation steps.
Objects exported from other packages
A bounded version of rnorm
A subrange version of runif
Determine simulation time from backbone
A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2021) <doi:10.1038/s41467-021-24152-2>.
Useful links