Cell Ranger
What is Cell Ranger?
Cell Ranger is a set of analysis pipelines for processing Chromium single cell data. It performs barcode processing and UMI counting to quantify gene expression (from 3', 5', and Flex assays), assembles V(D)J immune receptor sequences, and analyzes Feature Barcode data for applications such as cell surface protein analysis and sample multiplexing.
The cellranger mkfastq pipeline is deprecated in v10.0 and will be removed in a future release. Use Illumina’s BCL Convert to generate Cell Ranger-compatible FASTQ files.
Find your primary pipeline and learn how to use it
Select your library type(s) above, and we will guide you to the appropriate pipeline and corresponding documentation.
Algorithms overview
Overview of algorithms.
Advanced
Advanced pipeline content for Cell Ranger.
Release Notes
View the latest updates to Cell Ranger.
Q&A
Browse Q&As from the 10x Genomics support team.
Glossary
View terms and definitions relevant to Single Cell products.
Datasets
Access free public Chromium data from 10x Genomics.
Analysis Guides
A collection of introductions, tutorials, and blogs for data analysis beyond software.
Loupe Browser
Loupe Browser is a desktop application that allows you to interactively visualize data.