mito-utils 0.0.2

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

MiTo

This is the first release of MiTo: a python package for robust inference of mitochondrial clones and phylogenies. See also nf-MiTo, the companion Nextflow pipeline.

Documentation

A preliminary documentation of key functionalitites and APIs is available at MiTo Docs.

Installation

1. Install mamba (or conda)
2. Reproduce the environment with all needed dependencies at once, with:

mamba env create -f ./envs/environment.yml -n MiTo

3. Activate the environment, and manually install cassiopeia-lineage (no dependencies: it is all already present in the environment):

mamba activate MiTo
pip install --no-deps git+https://github.com/YosefLab/Cassiopeia.git@e7606afd10035a75f718ffb988666264e721700e

4. Install MiTo:

pip install mito-utils

5. Verify successfull installation:

import mito as mt

Releases

See CHANGELOG.md for a history of notable changes.