SCANPY: Large-scale Single-cell Gene Expression Data Analysis

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2018 Feb 8

PMID 29409532

Citations 2829

Authors

F Alexander Wolf

Philipp Angerer

Fabian J Theis

Affiliations

Soon will be listed here.

Abstract

SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells ( https://github.com/theislab/Scanpy ). Along with SCANPY, we present ANNDATA, a generic class for handling annotated data matrices ( https://github.com/theislab/anndata ).

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