DEPRECATED - PLEASE USE SCGENOME

scgenome: single cell whole genome analysis in python

scgenome is scalable python toolkit for analyzing single-cell whole genome data built on anndata and inspired by scanpy. scgenome includes preprocessing, visualization, and clustering functionality and can be used to analyze copy number, allele specific copy number, SNV and breakpoint features.

Installation

Installation from pypi is recommended:

pip install scgenome

We also recommend installing scgenome into a virtual environment using virtualenv. To create a fresh environment with scgenome use the following steps:

virtualenv venv
source venv/bin/activate
pip install scgenome

To install from source, clone this repo and use the following steps in the repo directory:

virtualenv venv
source venv/bin/activate
python setup.py develop

Documentation

Coming Soon

Pip build

To build with pip and distribute to pypi, use the following commands:

python setup.py build_ext --force sdist
twine upload --repository pypi dist/*

Build documentation

pip install -r docs/requirements/requirements.txt
pip install scgenome
cd docs
make html