Man pages for dyngen
A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses
| backbone | Backbone of the simulation model |
| backbone_models | List of all predefined backbone models |
| bblego | Design your own custom backbone easily |
| combine_models | Combine multiple dyngen models |
| convert | Convert simulation output to different formats. |
| dyngen | dyngen: A multi-modal simulator for spearheading single-cell... |
| 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 | Add small noise to the kinetics of each simulation |
| 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... |
| 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... |
| 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 |
| reexports | Objects exported from other packages |
| rnorm_bounded | A bounded version of rnorm |
| runif_subrange | A subrange version of runif |
| simtime_from_backbone | Determine simulation time from backbone |
