Single-Cell Analysis in Python.


Keywords
bioinformatics, data-science, genetics, machine-learning, transcriptomics, visualize-data
License
BSD-3-Clause
Install
pip install scanpy==1.3.8

Documentation

PyPI bioconda Docs Build Status

Scanpy – Single-Cell Analysis in Python

https://falexwolf.de/img/tsne_1.3M.png

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Read the documentation. If Scanpy is useful for your research, consider citing Genome Biology (2018).