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

Global functions
%>% Man page
.add_timing Source code
.download_cacheable_file Source code
.feature_network_fetch_realnet Source code
.feature_network_sample_downstream Source code
.generate_cells_precompile_reactions Source code
.generate_experiment_fetch_realcount Source code
.generate_experiment_sample_cells Source code
.generate_experiment_snapshot Source code
.generate_experiment_synchronised Source code
.generate_gold_standard_mod_changes Source code
.generate_partitions Source code
.generate_tf_info Source code
.generate_tf_network Source code
.kinetics_add_columns Source code
.kinetics_calculate_basal Source code
.kinetics_calculate_dissociation Source code
.kinetics_default_genes_sampler Source code
.kinetics_default_interactions_sampler Source code
.kinetics_extract_parameters Source code
.kinetics_extract_parameters_as_df Source code
.kinetics_generate_formulae Source code
.kinetics_generate_gene_kinetics Source code
.sample_decent_realcount Source code
.simulate_counts_from_realcounts Source code
as_anndata Man page Source code
as_dyno Man page Source code
as_list Man page Source code
as_sce Man page Source code
as_seurat Man page Source code
backbone Man page Source code
backbone_bifurcating Man page Source code
backbone_bifurcating_converging Man page Source code
backbone_bifurcating_cycle Man page Source code
backbone_bifurcating_loop Man page Source code
backbone_binary_tree Man page Source code
backbone_branching Man page Source code
backbone_consecutive_bifurcating Man page Source code
backbone_converging Man page Source code
backbone_cycle Man page Source code
backbone_cycle_simple Man page Source code
backbone_disconnected Man page Source code
backbone_linear Man page Source code
backbone_linear_simple Man page Source code
backbone_trifurcating Man page Source code
bblego Man page Source code
bblego_branching Man page
bblego_end Man page
bblego_linear Man page Source code
bblego_start Man page
calculate_dimred Source code
colour_brighten Source code
combine_models Man page Source code
dyngen Man page
effect_colour Source code
example_model Man page
experiment_snapshot Man page Source code
experiment_synchronised Man page Source code
feature_network_default Man page Source code
generate_cells Man page Source code
generate_dataset Man page Source code
generate_experiment Man page Source code
generate_feature_network Man page Source code
generate_gold_standard Man page Source code
generate_kinetics Man page Source code
generate_tf_network Man page Source code
get_timings Man page Source code
gold_standard_default Man page Source code
initialise_model Man page Source code
kinetics_default Man page Source code
kinetics_noise_none Man page Source code
kinetics_noise_simple Man page Source code
kinetics_random_distributions Man page Source code
list_backbones Man page Source code
list_experiment_samplers Man page Source code
modnet_chain Source code
modnet_edge Source code
modnet_pairwise Source code
modnet_self Source code
ode_em Man page
plot_backbone_modulenet Man page Source code
plot_backbone_statenet Man page Source code
plot_experiment_dimred Man page Source code
plot_feature_network Man page Source code
plot_gold_expression Man page Source code
plot_gold_mappings Man page Source code
plot_gold_simulations Man page Source code
plot_simulation_expression Man page Source code
plot_simulations Man page Source code
plot_timings Source code
realcounts Man page
realnets Man page
reexports Man page
rnorm_bounded Man page Source code
runif_subrange Man page Source code
simtime_from_backbone Man page Source code
simulation_default Man page Source code
simulation_type_knockdown Man page
simulation_type_wild_type Man page
ssa_etl Man page
ssa_exact Man page
tf_network_default Man page Source code
wrap_dataset Man page Source code
dyngen documentation built on April 13, 2021, 1:06 a.m.