synthetic: Synthetic benchmark data for mistyR

In saezlab/misty: Multiview Intercellular SpaTial modeling framework

Synthetic benchmark data for mistyR

Description

Data generated from 10 random layouts of four cell types and empty space on 100-by-100 grid by simulating a two-dimensional cellular automata model that focuses on signaling events. Cell growth, division, motility and death are neglected. The intracellular processes involve two layers, first the ligand activation of signaling hubs and ligand production/secretion regulated by proteins. The model simulates the production, diffusion, degradation and interactions of 11 molecular species. Ligands are produced in each cell-type based on the activity level of their production nodes and then freely diffuse, degrade or interact with other cells on the grid. Other molecular species involved in signaling are localised in the intracellular space and their activity depends on ligand binding and intracellular wiring.

Usage

data("synthetic")

Format

A named list of length 10. Each list item is a tibble that corresponds to a simulation of one random layout with information about each cell in rows described by the following 14 variables:

row, col

location of the cell on the grid

ligA, ligB, ligC, ligD

expression of ligands

protE, protF

expression of intracellular proteins

prodA, prodB, prodC, prodD

expression of regulatory proteins

type

cell type id

Source

https://github.com/saezlab/misty_pipelines/

saezlab/misty documentation built on March 25, 2024, 4:11 p.m.