lineageot 0.1.0

LineageOT

LineageOT

This code accompanies the paper https://biorxiv.org/cgi/content/short/2020.07.31.231621v2. Documentation is available at https://lineageot.readthedocs.io/.

Requirements and installation guide

Installing dependencies

First, clone this repository with

git clone https://github.com/aforr/LineageOT

Dependencies are listed in conda_requirements.yml as well as in pip_requirements.txt; earlier versions of the packages may work but have not been tested. If you are using Anaconda, they can be installed with

conda env create -f conda_requirements.yml

Installation may take a few minutes. Activate the environment with

conda activate lineageOT

If you are using pip and not Anaconda, install dependencies with

pip install numpy cython
pip install -r pip_requirements.txt

Installing LineageOT

Once you have set up and activated the environment, install the most recent LineageOT by running

pip install .

from the repository's base directory. Alternatively, install from PyPI with

pip install lineageot

No specific operating system is required, though there may be a bug in one of the dependencies in certain versions of MacOS (https://github.com/PythonOT/POT/issues/93). The code has been tested on OS X 10.14.6 and Ubuntu 16.04.

Examples

An example of LineageOT applied to simulated data is in examples/simulation_demo.ipynb. Running the notebook for one simulation type took around 10 minutes on a "normal" desktop.

To fit LineageOT couplings in your own system, follow the steps in examples/pipeline_demo.ipynb replacing the synthetic AnnData object with your data. We recommend then using the downstream analysis tools available in the Waddington-OT package: https://broadinstitute.github.io/wot/.