Cell Ranger

Cell Ranger is a cell analysis library for generate feature-barcode matrices, perform Analysis for RNA samples. Cell Ranger works in pipelines for it's RNA  sequencing analysis which allows it to: process raw sequencing output, read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis.

Availability and Restrictions


Cell Ranger is available on the Pitzer Cluster. The versions currently available at OSC are:

Version Pitzer Notes
7.0.0 X*  
7.2.0 X  
* Current Default Version

You can use module spider cellranger to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


Cell Ranger is available to only academic OSC users. Please review the license agreement and 10x Privacy Policy before use. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

The 10x Genomics group, Closed source (academic)


Usage on Pitzer


To configure your environment for use of Cell Ranger, run the following command: module load cellranger. The default version will be loaded. To select a particular Cell Ranger version, use module load cellranger/version. For example, use module load cellranger/7.0.0 to load Cell Ranger 7.0.0.

Further Reading

Fields of Science: