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

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Documentation for package ‘dyngen’ version 1.0.5

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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.