CBI Single Cell Analysis

The Cancer Bioinformatics (CBI) Shared Resource supports the analysis of 10x single cell experiments sequenced by the High-Throughput Genomics (HTG) Shared Resource. We can also assist with the analysis of single cell data from other sources and publicly available single cell datasets in NCBI GEO.

Resources

CBI builds automated pipelines to run cellranger, spaceranger and xeniumranger for data generated by Chromium, Visium and Xenium platforms from 10x Genomics. We carefully review the QC summaries and can help you explore results in the 10x Loupe browser. We have also developed a number of custom workflows to further analyze your single cell data using Seurat and many other software packages.

Our analysis services are highly customizable to the unique requirements of your single cell experiment. To date we have analyzed hundreds of single cell studies of gene expression, immune clonotypes, chromatin accessibility, multiome, multiplexed and spatial datasets. We also support the new HD spatial gene expression on Visium and targeted gene expression on a recently acquired Xenium platform.

If you are new to single cell sequencing, the resources tab on the 10x website provides links to datasets, publications, tutorials and software. Start by browsing the 10x datasets and download a Loupe file to explore expression data in the Loupe browser.

Please submit a help request or email us to discuss analysis options. If you need help with sample preparation and 10x sequencing, contact the HTG Shared Resource.