Data provided

We will try to provide data in a variety of formats for easy use. Additionally, the raw data for every study is made available through funding agency repositories (namely GEO, dbGaP, and/or EGA).

  • h5ad
    This is the standard output format from the Scanpy analysis toolkit. These files usually contain raw and normalized expression, gene and cell annotations like cluster labels and sample metadata, and dimesnionality reduction coordinates.
  • rds/rdata
    No matter the file extension here, these are rdata files, and contain (1) log-transformed, normalized expression, (2) a dataframe containing gene names and symbols, and (3) a dataframe containing t-SNE/UMAP coordinates and cluster labels.
    These are for use in our tool CellView.
  • loupe
    These files can be opened using the Loupe Cell Browser by 10X Genomics. We have modified these files to contain the same dimensionality reduction (typically labeled Custom_UMAP) and cluster labels (Custom Cluser) as used in the corresponding publication.
  • markers
    Unmodified lists of marker genes for a set of clusters computed in a one-vs-rest fashion.

Interactive exploration

Coming soon!

Get in touch

If you have any issues with the site or information presented here, please contact Bill Flynn.

Privacy Disclaimer

This website uses GoogleAnalytics to track page views and visitor counts. Please see The Jackson Laboratory's privacy policy.