Lineage Motif Analysis (LMA)

Schematic of LMA - Figure 2 from the paper

Table Of Contents

This documentation provides a guide for using Lineage Motif Analysis (LMA), a computational tool which analyzes a set of lineage trees to identify patterns of correlated cell fates that represent building blocks of larger developmental programs.

The walk-through consists of installation, API, and several tutorials, which showcase LMA applied to various lineage tree datasets.

Project Overview

The modules exported by this package include the following.

• 'resample': Resamples tree dataset and exports count of various kinds of cell fate patterns across all resamples, the original trees, and the expected number (solved analytically).
• 'plot': Visualize DataFrame outputs from 'resample' module as frequency or deviation plots.
• 'simulate': Simulate lineage trees with input progenitor/cell types and given transition matrix.

Acknowledgements

This project is supported by the Chen Graduate Innovator Award and NIH F31 (NEI) award to MT.