In dynverse/dyntoy: Generating simple toy data of cellular differentiation

knitr::opts_chunk$set(
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dyntoy

dyntoy simulates single-cell expression data in which a single-cell trajectory is present. Even though the model to generate the data is very simplistic (and far from realistic), it can simulate very complex trajectory models, such as large trees, convergences and loops.

As the data is relatively easy, it can be used to quickly test and prototype a TI method. However, for more realistic synthetic data, check out our dyngen package.

Installation

Install using devtools:

# install.packages("devtools")
devtools::install_github("dynverse/dyntoy")

Example

dyntoy contains some pre-generated toy data within the toy_datasets data object:

data("toy_datasets", package = "dyntoy")

Data can be generated using generate_dataset:

library(dyntoy)
dataset <- generate_dataset(
  model = model_bifurcating(),
  num_cells = 1000,
  num_features = 1000
)

dataset$milestone_network

Related work

• PROSSTT: https://github.com/soedinglab/prosstt
• Splatter: https://github.com/Oshlack/splatter

Latest changes

Check out news(package = "dyntoy") or NEWS.md for a full list of changes.

dynutils::update_news()
cat(dynutils::recent_news())

Dynverse dependencies

dynverse/dyntoy documentation built on May 25, 2019, 4:26 p.m.