Learn R Programming

SITH (version 1.1.0)

A Spatial Model of Intra-Tumor Heterogeneity

Description

Implements a three-dimensional stochastic model of cancer growth and mutation similar to the one described in Waclaw et al. (2015) . Allows for interactive 3D visualizations of the simulated tumor. Provides a comprehensive summary of the spatial distribution of mutants within the tumor. Contains functions which create synthetic sequencing datasets from the generated tumor.

Copy Link

Version

Install

install.packages('SITH')

Monthly Downloads

187

Version

1.1.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/phillipnicol/SITH

Maintainer

Phillip Nicol

Last Published

January 5th, 2021

Functions in SITH (1.1.0)

randomSingleCells

Simulate single cell sequencing data

Simulate fine needle aspiration

randomBulkSamples

Simulate multi-region bulk sampling

Spatial simulation of tumor growth

Simulate single cell sequencing data

progressionDAG_from_igraph

Define the progression of mutations from an igraph object

2D cross section of the simulated tumor

Visualize and analyze intratumor heterogeneity using a spatial model of tumor growth

spatialDistribution

Quantify the spatial distribution of mutants

Interactive visualization of the simulated tumor

Simulate bulk sampling

progressionChain

Create a linear chain graph to describe the order of mutations