10x Genomics Support/

Cell Ranger

software-intro
What is Cell Ranger?

A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.

Download Cell RangerGet Started with Cell Ranger

Cell Ranger v8.0 introduces support for the analysis of GEM-X libraries.
Cell Ranger v7.2 is the last version to support the analysis of LT (low throughput) libraries.

Analysis

Inputs

Learn more about input files required to run Cell Ranger

Running Pipelines

Learn more about how to run Cell Ranger

Outputs

Learn more about the output files generated by Cell Ranger

Tutorials

Get Started with Cell Ranger
Cell Ranger installation
Cell Ranger mkfastq
Convert BCL to FASTQ with Cell Ranger mkfastq
Cell Ranger count
Analyze Gene Expression and Feature Barcode data with Cell Ranger count
View all tutorials

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.