mito-utils 0.0.1

Utilities for MT-based single cell Lineage Tracing (scLT).

MiTo

This is the first release of MiTo: robust inference of mitochondrial clones and phylogenies.

Documentation

See ... for a comprehensive description of key functionalitites, main APIs, and tutorials.

Installation

1. Install mamba (or conda) package manager (https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
2. Reproduce the necessary computational environment with:

mamba env create -f ./envs/environment.yml -n <your conda env name>

3. Activate the environment, and manually install cassiopeia-lineage (no dependencies: all has been already installed in the environment. Sometimes pip messes with cassipeia dependencies trying to re-install them).

mamba activate <your conda env name>
pip install --no-deps git+https://github.com/YosefLab/Cassiopeia.git@e7606afd10035a75f718ffb988666264e721700e

4. Install MiTo:

pip install mito==0.0.1

5. Verify successfull installation:

import mito as mt

Releases

See CHANGELOG.md for a history of notable changes.