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. |