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dyngen 1.0.5

  • MINOR CHANGE: Refactor matrix coercion thanks to Matrix 1.5-0.

  • DOCUMENTATION: Remove comments from generate_dataset().

  • DOCUMENTATION: Extend usage of wrap_dataset().

  • DOCUMENTATION: Document outputs of combine_models() and get_timings().

  • BUG FIX calculate_dimred(): Force deep copy of matrix to avoid error message: "Error in x$.self$finalize() : attempt to apply non-function".

dyngen 1.0.4

  • BUG FIX plot_feature_network(): Added workaround for thomasp85/ggforce#273.

dyngen 1.0.3

  • BUG FIX generate_experiment(): Return timepoint groups for experiment_synchronised().

  • BUG FIX unit tests: loosen generate partitions constraints.

dyngen 1.0.2

  • MINOR CHANGE generate_dataset(): Fix subplot title.

  • NEW FEATURE plot_summary(): Create a dedicated function for plotting a dyngen summary.

  • BUG FIX generate_cells(): Fix incorrect cell count when one of the backbone segments does not have any simulations steps (#26).

  • DOCUMENTATION: Update citation to NCOMMS publication.

dyngen 1.0.1

  • MINOR CHANGE .download_cacheable_file(): Check the return value of utils::download.file(), since it is possible that the download will fail with a non-zero status but not an R error.

  • MINOR CHANGE kinetics_random_distributions(): Add function for providing randomised distributions.

dyngen 1.0.0

This version mostly upgrades dyngen's ease-of-use, such as better vignettes, conversion functions for working with dyngen datasets in other packages, and more useful ways of specifying platform-specific parameters (i.e. number of cores and cache location). Perhaps more excitingly, the dyngen documentation is more readable online at https://dyngen.dynverse.org!

BREAKING CHANGES

  • wrap_dataset(): Now returns a list instead of a dyno object. Use as_dyno(model) or wrap_dataset(model, format = "dyno") to replicate previous behaviour.

NEW FEATURES

  • Added functions for converting the dyngen output to various data formats: as_anndata() for anndata, as_sce() for SingleCellExperiment, as_seurat() for Seurat, as_dyno() for dyno, as_list() for a simple list object.

  • wrap_dataset(): Added 'format' argument which allows choosing the output format (#28).

  • The default number of cores used can be set by adding options(Ncpus = ...) to your Rprofile.

  • The default cache folder for dyngen can be set by adding options(dyngen_download_cache_dir = ...) to your Rprofile.

  • Combine similar models with different outputs using the combine_models() function.

  • Store the timings throughout the dyngen execution. Extract the timings from a model using get_timings().

MAJOR CHANGES

  • generate_experiment(): Map count density of reference dataset to simulation expression before sampling molecules. Parameters are available for toggling off or on the mapping of the reference library size & CPM distribution.

MINOR CHANGES

  • initialise_model(): Change defaults of num_cores and download_cache_dir to getOption("Ncpus") and getOption("dyngen_download_cache_dir") respectively.

  • generate_experiment(): Drastically speed up sampling of molecules.

BUG FIX

  • as_dyno(): Fix drop = FALSE bug when only one cell is being sampled.

  • Removed names from feature ids in feature info (unname(model$feature_info$feature_id)). Thanks @milanmlft!

DOCUMENTATION

  • Added and extended vignettes:

    • Advanced: Simulating batch effects
    • Advanced: Simulating a knockout experiment
    • Advanced: Running dyngen from a docker container
    • Advanced: Constructing a custom backbone
    • Advanced: Tweaking parameters
    • Advanced: Comparison of characteristic features between dyngen and reference datasets

  • Created a website at https://dyngen.dynverse.org using pkgdown.

  • Shortened examples to reduce r cmd check time.

dyngen 0.4.0

MAJOR CHANGES

  • wrap_dataset(): Outputted $counts now contains counts of both spliced and unspliced reads, whereas $counts_unspliced and $counts_spliced contains separated counts.

  • Added a docker container containing the necessary code to run a dyngen simulation.

MINOR CHANGES

  • Added logo to package.

  • Clean up internal code, mostly to satisfy R CMD check.

DOCUMENTATION

  • Added two vignettes.

  • Expanded the README.

dyngen 0.3.0 (2020-04-06)

NEW FEATURES

  • Implement knockdown / knockouts / overexpression experiments.

  • Implement better single-cell regulatory activity by determining the effect on propensity values after knocking out a transcription factor.

  • Implement adding noise to the kinetic params of individual simulations.

  • Kinetics (transcription rate, translation rate, decay rate, ...) are based on Schwannhausser et al. 2011.

  • Changed many parameter names to better explain its purpose.

MINOR CHANGES

  • Fix module naming of backbones derived from backbone_branching().

  • Allow to plot labels in plot_simulation_expression().

  • Improve backbone_disconnected() and backbone_converging().

  • Rename required columns in backbone() input data.

  • Use backbone_linear() to make backbone_cyclic() randomised.

  • Added a decay rate for pre-mRNAs as well.

  • Kinetics: redefine the decay rates in terms of the half-life of these molecules.

  • Only compute dimred if desired.

  • Allow computing the propensity ratios as ground-truth for rna velocity.

BUG FIXES

  • Implement fix for double positives in bblego backbones.

  • Fix graph plotting mixup of interaction effects (up/down).

  • Made a fix to the computation of feature_info$max_protein.

dyngen 0.2.1 (2019-07-17)

  • MAJOR CHANGES: Custom backbones can be defined using backbone lego pieces. See ?bblego for more information.

  • MAJOR CHANGES: Splicing reactions have been reworked to better reflect biology.

dyngen 0.2.0 (2019-07-12)

Complete rewrite from dyngen from the bottom up.

  • OPTIMISATION: All aspects of the pipeline have been optimised towards execution time and end-user usability.

  • OPTIMISATION: dyngen 0.2.0 uses gillespie 0.2.0, which has also been rewritten entirely in Rcpp, thereby improving the speed significantly.

  • OPTIMISATION: The transcription factor propensity functions have been refactored to make it much more computationally efficient.

  • OPTIMISATION: Mapping a simulation to the gold standard is more automised and less error-prone.

  • FEATURE: A splicing step has been added to the chain of reaction events.

dyngen 0.1.0 (2017-04-27)

  • INITIAL RELEASE: a package for generating synthetic single-cell data from regulatory networks. Key features are:

    • The cells undergo a dynamic process throughout the simulation.
    • Many different trajectory types are supported.
    • dyngen 0.1.0 uses gillespie 0.1.0, a clone of GillespieSSA that is much less error-prone and more efficient than GillespieSSA.

dyngen 0.0.1 (2016-04-04)

  • Just a bunch of scripts on a repository, which creates random networks using igraph and generates simple single-cell expression data using GillespieSSA.