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UCSC Single Cell Browser

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

If you want us to add a single cell dataset to the website http://cells.ucsc.edu, please contact us at cells@ucsc.edu. We are happy to add any dataset.

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 Scope.

Many labs host their data at cells.ucsc.edu by sending it to us, but some groups have setup their own cell browsers:

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 cells@ucsc.edu, 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.

Additional availability

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 cells@ucsc.edu, we can usually fix them quickly.

Citation

If you use the UCSC Cell Browser in your work, please cite Speir et al, Biorxiv 2020