UCSC Cell Browser: visualize your single-cell data

Matthew L Speir; Aparna Bhaduri; Nikolay S Markov; Pablo Moreno; Tomasz J Nowakowski; Irene Papatheodorou; Alex A Pollen; Brian J Raney; Lucas Seninge; W James Kent; Maximilian Haeussler

doi:10.1093/bioinformatics/btab503

UCSC Cell Browser: visualize your single-cell data

Bioinformatics. 2021 Dec 7;37(23):4578-4580. doi: 10.1093/bioinformatics/btab503.

Authors

Matthew L Speir¹, Aparna Bhaduri², Nikolay S Markov³, Pablo Moreno⁴, Tomasz J Nowakowski^{5

6

7

8}, Irene Papatheodorou⁴, Alex A Pollen^{5

9}, Brian J Raney¹, Lucas Seninge^{1

10}, W James Kent¹, Maximilian Haeussler¹

Affiliations

¹ Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
² Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA.
³ Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
⁴ EMBL-EBI European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁵ The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA.
⁶ Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.
⁷ Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
⁸ Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
⁹ Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA.
¹⁰ Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

Abstract

Summary: As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.

Availability and implementation: We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

UCSC Cell Browser: visualize your single-cell data

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