Package: dyngen 1.1.1

Robrecht Cannoodt

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

A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2021) <doi:10.1038/s41467-021-24152-2>.

Authors:Robrecht Cannoodt [aut, cre, cph], Wouter Saelens [aut]

dyngen_1.1.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dyngen/json (API)

# Install 'dyngen' in R:
install.packages('dyngen', repos = c('https://dynverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dynverse/dyngen/issues

Pkgdown/docs site:https://dyngen.dynverse.org

Datasets:
  • example_model - A (very!) small toy dyngen model
  • realcounts - A set of real single cell expression datasets
  • realnets - A set of gold standard gene regulatory networks

On CRAN:

Conda:

benchmarkingsingle-cellsingle-cell-analysissingle-cell-omics

8.05 score 80 stars 88 scripts 680 downloads 2 mentions 66 exports 71 dependencies

Last updated from:620b3e8fab. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK278
source / vignettesOK319
linux-release-x86_64OK243
macos-release-arm64OK200
macos-oldrel-arm64OK164
windows-develOK217
windows-releaseOK194
windows-oldrelOK213
wasm-releaseOK215

Exports:as_anndataas_dynoas_listas_sceas_seuratbackbonebackbone_bifurcatingbackbone_bifurcating_convergingbackbone_bifurcating_cyclebackbone_bifurcating_loopbackbone_binary_treebackbone_branchingbackbone_consecutive_bifurcatingbackbone_convergingbackbone_cyclebackbone_cycle_simplebackbone_disconnectedbackbone_linearbackbone_linear_simplebackbone_trifurcatingbblegobblego_branchingbblego_endbblego_linearbblego_startcombine_modelsexperiment_snapshotexperiment_synchronisedfeature_network_defaultgenerate_cellsgenerate_datasetgenerate_experimentgenerate_feature_networkgenerate_gold_standardgenerate_kineticsgenerate_tf_networkget_timingsgold_standard_defaultinitialise_modelkinetics_defaultkinetics_noise_nonekinetics_noise_simplekinetics_random_distributionslist_backboneslist_experiment_samplersode_emplot_backbone_modulenetplot_backbone_statenetplot_experiment_dimredplot_feature_networkplot_gold_expressionplot_gold_mappingsplot_gold_simulationsplot_simulation_expressionplot_simulationsplot_summaryrnorm_boundedrunif_subrangesimtime_from_backbonesimulation_defaultsimulation_type_knockdownsimulation_type_wild_typessa_etlssa_exacttf_network_defaultwrap_dataset

Dependencies:assertthatbase64encbitbit64cachemclicliprcpp11crayondescdplyrdynutilsfarverfastmapgenericsggforceggplot2ggraphggrepelGillespieSSA2gluegraphlayoutsgridExtragtablehmsigraphirlbaisobandjsonlitelabelinglatticelifecyclelmdsmagrittrMASSMatrixmemoisepatchworkpbapplypillarpkgconfigpolyclipprettyunitsprogressproxyCpurrrR6RColorBrewerRcppRcppArmadilloRcppXPtrUtilsreadrremotesrlangS7scalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrtzdbutf8vctrsviridisviridisLitevroomwithr

Installation instructions
System requirements | Step 1: Installing from CRAN or GitHub (Required) | Step 2: Configure host system (Recommended) | Step 3: Download cacheable files (Optional)
Rendered frominstallation.html.asisusingR.rsp::asis

Last update: 2021-02-23
Started: 2021-02-23

Getting started
Step 1: Define backbone and other parameters | Step 2: Generate transcription factors (TFs) | Step 3: Sample target genes and housekeeping genes (HKs) | Step 4: Generate kinetics | Step 5: Simulate gold standard | Step 6: Simulate cells. | Step 7: Experiment emulation | Step 8: Convert to a dyno object | Step 8 alternative: Convert to an anndata/SCE/Seurat object | One-shot function
Rendered fromgetting_started.html.asisusingR.rsp::asis

Last update: 2020-07-15
Started: 2020-07-15

Readme and manuals

Help Manual

Help pageTopics
dyngen: A multi-modal simulator for spearheading single-cell omics analysesdyngen-package dyngen
Convert simulation output to different formats.as_anndata as_dyno as_list as_sce as_seurat wrap_dataset
Backbone of the simulation modelbackbone
Design your own custom backbone easilybblego bblego_branching bblego_end bblego_linear bblego_start
Combine multiple dyngen modelscombine_models
A (very!) small toy dyngen modelexample_model
Simulate the cellsgenerate_cells simulation_default simulation_type_knockdown simulation_type_wild_type
Generate a datasetgenerate_dataset
Sample cells from the simulationsexperiment_snapshot experiment_synchronised generate_experiment list_experiment_samplers
Generate a target networkfeature_network_default generate_feature_network
Simulate the gold standardgenerate_gold_standard gold_standard_default
Determine the kinetics of the feature networkgenerate_kinetics kinetics_default kinetics_random_distributions
Generate a transcription factor network from the backbonegenerate_tf_network tf_network_default
Return the timings of each of the dyngen stepsget_timings
Initial settings for simulating a dyngen datasetinitialise_model
Add small noise to the kinetics of each simulationkinetics_noise_none kinetics_noise_simple
List of all predefined backbone modelsbackbone_bifurcating backbone_bifurcating_converging backbone_bifurcating_cycle backbone_bifurcating_loop backbone_binary_tree backbone_branching backbone_consecutive_bifurcating backbone_converging backbone_cycle backbone_cycle_simple backbone_disconnected backbone_linear backbone_linear_simple backbone_trifurcating list_backbones
Visualise the backbone of a modelplot_backbone_modulenet
Visualise the backbone state network of a modelplot_backbone_statenet
Plot a dimensionality reduction of the final datasetplot_experiment_dimred
Visualise the feature network of a modelplot_feature_network
Visualise the expression of the gold standard over simulation timeplot_gold_expression
Visualise the mapping of the simulations to the gold standardplot_gold_mappings
Visualise the simulations using the dimredplot_gold_simulations
Visualise the expression of the simulations over simulation timeplot_simulation_expression
Visualise the simulations using the dimredplot_simulations
Plot a summary of all dyngen simulation steps.plot_summary
A set of real single cell expression datasetsrealcounts
A set of gold standard gene regulatory networksrealnets
A bounded version of rnormrnorm_bounded
A subrange version of runifrunif_subrange
Determine simulation time from backbonesimtime_from_backbone