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

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Documentation for package ‘dyngen’ version 1.0.5

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

Help Pages

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.