as_dyno                 Convert simulation output to different formats.
backbone                Backbone of the simulation model
bblego                  Design your own custom backbone easily
combine_models          Combine multiple dyngen models
dyngen                  dyngen: A multi-modal simulator for
                        spearheading single-cell omics analyses
example_model           A (very!) small toy dyngen model
generate_cells          Simulate the cells
generate_dataset        Generate a dataset
generate_experiment     Sample cells from the simulations
generate_feature_network
                        Generate a target network
generate_gold_standard
                        Simulate the gold standard
generate_kinetics       Determine the kinetics of the feature network
generate_tf_network     Generate a transcription factor network from
                        the backbone
get_timings             Return the timings of each of the dyngen steps
initialise_model        Initial settings for simulating a dyngen
                        dataset
kinetics_noise_none     Add small noise to the kinetics of each
                        simulation
list_backbones          List of all predefined backbone models
plot_backbone_modulenet
                        Visualise the backbone of a model
plot_backbone_statenet
                        Visualise the backbone state network of a model
plot_experiment_dimred
                        Plot a dimensionality reduction of the final
                        dataset
plot_feature_network    Visualise the feature network of a model
plot_gold_expression    Visualise the expression of the gold standard
                        over simulation time
plot_gold_mappings      Visualise the mapping of the simulations to the
                        gold standard
plot_gold_simulations   Visualise the simulations using the dimred
plot_simulation_expression
                        Visualise the expression of the simulations
                        over simulation time
plot_simulations        Visualise the simulations using the dimred
plot_summary            Plot a summary of all dyngen simulation steps.
realcounts              A set of real single cell expression datasets
realnets                A set of gold standard gene regulatory networks
rnorm_bounded           A bounded version of rnorm
runif_subrange          A subrange version of runif
simtime_from_backbone   Determine simulation time from backbone
