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_pkgdown.yml
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url: https://dyngen.dynverse.org
home:
links:
- text: Publication
href: "https://doi.org/10.1038/s41467-021-24152-2"
template:
params:
ganalytics: "G-7YGMM4L0JM"
articles:
- title: Getting started with dyngen
navbar: ~
contents:
- installation
- getting_started
- showcase_backbones
- title: Advanced topics
navbar: Advanced
contents:
- starts_with("advanced")
reference:
- title: Step 1, initialise dyngen model
desc: Define and store settings for all following steps. See each of the sections below for more information.
- contents:
- initialise_model
- list_backbones
- starts_with("backbone")
- starts_with("bblego")
- plot_backbone_modulenet
- plot_backbone_statenet
- title: Step 2, generate TF network
desc: Generate a transcription factor network from the backbone
- contents:
- generate_tf_network
- tf_network_default
- title: Step 3, add more genes to the gene network
desc: Generate a target network
- contents:
- generate_feature_network
- feature_network_default
- plot_feature_network
- title: Step 4, generate gene kinetics
desc: Generate kinetics from each gene in the network
- contents:
- generate_kinetics
- kinetics_default
- kinetics_random_distributions
- title: Step 5, simulate the gold standard
desc: Simulate the gold standard backbone, used for mapping to cell states afterwards
- contents:
- generate_gold_standard
- gold_standard_default
- plot_gold_mappings
- plot_gold_simulations
- plot_gold_expression
- title: Step 6, simulate the cells
desc: Simulate the cells based on its GRN
- contents:
- generate_cells
- simulation_default
- starts_with("simulation_type_")
- plot_simulations
- plot_simulation_expression
- title: Step 7, simulate cell and transcripting sampling
desc: Simulate cell and transcripting sampling
- contents:
- generate_experiment
- list_experiment_samplers
- experiment_snapshot
- experiment_synchronised
- kinetics_noise_none
- kinetics_noise_simple
- simtime_from_backbone
- plot_experiment_dimred
- title: Step 8, convert to dataset
desc: Convert to a dataset object for ease of use
- contents:
- wrap_dataset
- as_dyno
- as_anndata
- as_sce
- as_seurat
- title: One-shot function
desc: Run through steps 2 to 8 with a single function
- contents:
- generate_dataset
- plot_summary
- title: Data objects
- contents:
- example_model
- realcounts
- realnets
- title: Varia functions
- contents:
- dyngen
- get_timings
- combine_models
- rnorm_bounded
- runif_subrange