Metadata-Version: 2.1
Name: lineageot
Version: 0.1.0
Summary: LineageOT
Home-page: https://github.com/aforr/LineageOT
Author: Aden Forrow
Author-email: aden.forrow@maths.ox.ac.uk
License: UNKNOWN
Description: # 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/.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
