The UCSC Cell Browser is a viewer for single cell data. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster-specific marker genes.
To look at a list of selected single cell datasets, see http://cells.ucsc.edu
To setup your own cell browser, from Cellranger, Seurat, Scanpy or text files (tsv/csv), or just a single cell expression matrix, read the documentation at http://cellbrowser.rtfd.io
This is a viewer for a static, precomputed layout. If you're looking for an interative layout, where you can
move the cells around and run some algorithms interactively, try Chan-Zuckerberg's own cellxgene or Spring.
A website with both datasets and some analysis is
Many labs host their data at cells.ucsc.edu by sending it to us, but some groups have setup their own cell browsers:
Zhang et al. 2018 <https://www.biorxiv.org/content/10.1101/351130v1>and
Der et al 2018 <https://www.biorxiv.org/content/10.1101/382846v1>
Croft et al, Nature 2019 <https://www.nature.com/articles/s41586-019-1263-7>_
STAB: a spatio-temporal cell atlas of the human brain <https://stab.comp-sysbio.org/tool/cellbrowser/index.html>from
Song et al NAR 2021 <https://academic.oup.com/nar/article/49/D1/D1029/5911746>.
Collins et al. 2021. The Ocular Surface. <https://www.sciencedirect.com/science/article/pii/S1542012421000215>_
These papers have cell browsers made at UCSC:
Before judging this project by the number of issue tickets or PRs, note that at UCSC we use an internal ticket system with more features and that a lot of communication with wetlab users is by email at firstname.lastname@example.org, as we do not require a Github account for feedback. But we do reply to issues here, as you can see from the Github account and also use Github for source control.
bioconda <https://bioconda.github.io/recipes/ucsc-cell-browser/README.html>_. Note that the conda release is usually a bit outdated relative to the pip release, so use pip if possible. If you cannot use pip, please contact us.
Galaxy Toolshed entry <https://toolshed.g2.bx.psu.edu/view/ebi-gxa/ucsc_cell_browser>or it can be directly used by users at the
Human Cell Atlas Galaxy instance <https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/ucsc_cell_browser/ucsc_cell_browser>or as part of the example workflows, such as the
Human Cell Atlas / Scanpy CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/humancellatlas-scanpy-cellbrowser>or the
EBI Single Cell Expression Atlas / Scanpy / CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/atlas-scanpy-cellbrowser-imported-from-uploaded-file>
This project was funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/. In 2020, it is funded through a supplement to the NHGRI Genome Browser grant.
This is early research software. You are likely to find bugs. Please open a Github ticket or email us at email@example.com, we can usually fix them quickly.
If you use the UCSC Cell Browser in your work, please cite
Speir et al, Biorxiv 2020 <https://www.biorxiv.org/content/10.1101/2020.10.30.361162v1>_