CellRanger 3.1.0

There is a newer version of CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.

Accessing CellRanger 3.1.0

To load the module for CellRanger 3.1.0 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load CellRanger/3.1.0

BEAR Apps Version


CellRanger Reference Data

The Cell Ranger reference data sets and these are available in ${BB_APPS_DATA}/CellRanger/

CellRanger and bcl2fastq

Please note that some of the CellRanger pipelines (e.g. cellranger mkfastq) require the use of another application: bcl2fastq. If required, please select a version bcl2fastq2 to use.

More Information

For more information visit the CellRanger website.


This version of CellRanger has a direct dependency on: Java/1.8

Other Versions

These versions of CellRanger are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Version BEAR Apps Version
7.1.0 2022a
7.0.0 2021a
6.0.1 2020b
5.0.1 2020a
3.0.2 2018b

Last modified on 3rd October 2019