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
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 algorithsm interactively, try Chan-Zuckerberg's own cellxgene or Spring.
Apart from labs at UCSC, UCSF and Gladstone who host their data at cells.ucsc.edu, other groups have setup their own cell browsers:
- Alexander Misharin Lab, Northwester University, https://www.nupulmonary.org/resources/
- Accelerating Medicine Partnership Consortium, https://immunogenomics.io/cellbrowser/, used in <a href="https://www.biorxiv.org/content/10.1101/351130v1">Zhang et al. 2018</a> and <a href="https://www.biorxiv.org/content/10.1101/382846v1">Der et al. 2018</a>
Funded by the California Institute of Regenerative Medicine and the Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/.
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.