Step 1, initialise dyngen modelDefine and store settings for all following steps. See each of the sections below for more information. |
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Initial settings for simulating a dyngen dataset |
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List of all predefined backbone models |
Backbone of the simulation model |
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Design your own custom backbone easily |
Visualise the backbone of a model |
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Visualise the backbone state network of a model |
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Step 2, generate TF networkGenerate a transcription factor network from the backbone |
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Generate a transcription factor network from the backbone |
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Step 3, add more genes to the gene networkGenerate a target network |
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Generate a target network |
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Visualise the feature network of a model |
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Step 4, generate gene kineticsGenerate kinetics from each gene in the network |
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Determine the kinetics of the feature network |
Step 5, simulate the gold standardSimulate the gold standard backbone, used for mapping to cell states afterwards |
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Simulate the gold standard |
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Visualise the mapping of the simulations to the gold standard |
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Visualise the simulations using the dimred |
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Visualise the expression of the gold standard over simulation time |
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Step 6, simulate the cellsSimulate the cells based on its GRN |
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Simulate the cells |
Visualise the simulations using the dimred |
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Visualise the expression of the simulations over simulation time |
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Step 7, simulate cell and transcripting samplingSimulate cell and transcripting sampling |
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Sample cells from the simulations |
Add small noise to the kinetics of each simulation |
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Determine simulation time from backbone |
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Plot a dimensionality reduction of the final dataset |
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Step 8, convert to datasetConvert to a dataset object for ease of use |
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Convert simulation output to different formats. |
One-shot functionRun through steps 2 to 8 with a single function |
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Generate a dataset |
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Plot a summary of all dyngen simulation steps. |
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Data objects |
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A (very!) small toy dyngen model |
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A set of real single cell expression datasets |
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A set of gold standard gene regulatory networks |
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Varia functions |
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dyngen: A multi-modal simulator for spearheading single-cell omics analyses |
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Return the timings of each of the dyngen steps |
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Combine multiple dyngen models |
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A bounded version of rnorm |
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A subrange version of runif |