# A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses

## Documentation for package ‘dyngen’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

dyngen-package | dyngen: A multi-modal simulator for spearheading single-cell omics analyses
as_anndata | Convert simulation output to different formats.
as_dyno | Convert simulation output to different formats.
as_list | Convert simulation output to different formats.
as_sce | Convert simulation output to different formats.
as_seurat | Convert simulation output to different formats.
backbone | Backbone of the simulation model
backbone_bifurcating | List of all predefined backbone models
backbone_bifurcating_converging | List of all predefined backbone models
backbone_bifurcating_cycle | List of all predefined backbone models
backbone_bifurcating_loop | List of all predefined backbone models
backbone_binary_tree | List of all predefined backbone models
backbone_branching | List of all predefined backbone models
backbone_consecutive_bifurcating | List of all predefined backbone models
backbone_converging | List of all predefined backbone models
backbone_cycle | List of all predefined backbone models
backbone_cycle_simple | List of all predefined backbone models
backbone_disconnected | List of all predefined backbone models
backbone_linear | List of all predefined backbone models
backbone_linear_simple | List of all predefined backbone models
backbone_trifurcating | List of all predefined backbone models
bblego | Design your own custom backbone easily
bblego_branching | Design your own custom backbone easily
bblego_end | Design your own custom backbone easily
bblego_linear | Design your own custom backbone easily
bblego_start | 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
experiment_snapshot | Sample cells from the simulations
experiment_synchronised | Sample cells from the simulations
feature_network_default | Generate a target network
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
gold_standard_default | Simulate the gold standard
initialise_model | Initial settings for simulating a dyngen dataset
kinetics_default | Determine the kinetics of the feature network
kinetics_noise_none | Add small noise to the kinetics of each simulation
kinetics_noise_simple | Add small noise to the kinetics of each simulation
kinetics_random_distributions | Determine the kinetics of the feature network
list_backbones | List of all predefined backbone models
list_experiment_samplers | Sample cells from the simulations
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_simulations | Visualise the simulations using the dimred
plot_simulation_expression | Visualise the expression of the simulations over simulation time
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
simulation_default | Simulate the cells
simulation_type_knockdown | Simulate the cells
simulation_type_wild_type | Simulate the cells
tf_network_default | Generate a transcription factor network from the backbone
wrap_dataset | Convert simulation output to different formats.