SCANPY: large-scale single-cell gene expression data analysis

Other free copies

• Cold Spring Harbor Laboratory (biorxiv.org)Accepted manuscript · PDF
• National Institutes of Health (ncbi.nlm.nih.gov)Preprint · Web page
• doaj.orgPreprint · Web page
• push-zb.helmholtz-muenchen.dePreprint · Web page

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 ).