v7.2.0 (Sept 13, 2023)

v7.1.0 (Dec 7, 2022)

v7.0.1 (Aug 18, 2022)

v7.0.0 (May 17, 2022)

v6.1.2 (Oct 25, 2021)

v6.1.1 (Aug 12, 2021)

v6.1.0 (Aug 9, 2021)

v6.0.2 (June 16, 2021)

v6.0.1 (April 13, 2021)

v6.0.0 (March 2, 2021)

v5.0.1 (Dec 16, 2020)

v5.0.0 (Nov 19, 2020)

v4.0.0 (July 7, 2020)

v3.1

v3.0.2

v3.0.1

v3.0.0

v2.2.0

v2.1.1

v2.1.0

v2.0.2

v2.0.1

v2.0.0

v1.3.1

v1.3.0

v1.2.1

v1.2.0

v1.1.0

v1.0.1

v1.0.0

Cell Ranger

Chromium

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression and multiomic capabilities to profile tens of thousands of cells. Explore cellular heterogeneity, novel targets, and biomarkers with combined gene expression, cell surface protein expression, or CRISPR edits in each cell.

Cell Surface Protein

CRISPR Screening

Sample multiplexing

Reveal the full complexity of cellular diversity, <em>cell by cell</em>

Chromium X Series

Advanced system for multiomic analysis of hundreds to millions of cells.

Single Cell Gene Expression

3' gene expression profiling at scale with single cell resolution.

Chromium Single Cell Immune Profiling provides a multiomic solution to your immunology questions. Analyze full-length V(D)J sequences for paired B-cell or T-cell receptors, cell surface protein expression, antigen specificity, and/or CRISPR edits, along with gene expression, all from a single cell.

Antigen Specificity

Multiomic profiling of immune diversity, <em>cell by cell</em>

Single Cell Immune Profiling

5' gene expression alongside V(D)J repertoire profiling and antigen specificity of T and B cells.

Profile a defined set of transcripts from single cells or tissue sections with Targeted Gene Expression. Reduce costs while increasing the number of samples, or increasing sequencing depth with customizable, comprehensive gene panels.

Discontinuation of Targeted Gene Expression

Chromium Connect

Automated system for single cell partitioning, barcoding, and library preparation.

Chromium Controller

Compact system for multiomic analysis of hundreds to tens of thousands of single cells.

Targeted Gene Expression

Visium

Profiling of defined transcript sets from single cells or fresh frozen tissue sections.

Analyze single cell gene expression data with a set of free, easy-to-use analysis pipelines.

Release Notes for 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.

Overview

Getting Started

Download Center

Cell Ranger Commands

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Miscellaneous

Release Notes

Glossary

Datasets

Loupe Browser

Cell Ranger 7.2

Installation

Get Started with Cell Ranger

Analyze Gene Expression and Feature Barcode data with Cell Ranger count

count

Cell Ranger count

aggr

Cell Ranger aggr

Rerun secondary analysis for a completed cellranger count or aggr run with different parameters

reanalyze

Cell Ranger reanalyze

Build a custom reference using Cell Ranger mkref

mkref

Cell Ranger mkref

Analyze cell multiplexing data with Cell Ranger multi

multi

Cell Ranger multi for 3' Cell Multiplexing

Analyze V(D)J and 5' GEX with Cell Ranger multi

multi for V(D)J

Cell Ranger multi for Immune Profiling

Analyze your GEX + VDJ + B cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-Ab

Analyze your GEX + VDJ + T cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-T

Analyze V(D)J libraries with Cell Ranger vdj

Cell Ranger vdj

Capturing Neutrophils in 10x Single Cell Gene Expression Data

Capturing neutrophils

Capturing Neutrophils

Analyze scRNA-Seq Data From a Publication Using 10x Software

Data analysis

Example Data Analysis

Analysis and visualization of data in the tumor microenvironment application note using the Loupe and Loupe V(D)J Browsers

Characterize tumor cells

Tumor Microenvironment Data Analysis and Visualization

Understand pipeline telemetry data collection and learn how to disable it if needed

Cell Ranger Pipeline Telemetry

View all tutorials

We provide resources from protocols, user guides, and free-to-use analysis tools

Learn more about input files required to run Cell Ranger

Inputs

Inputs Overview

Generating FASTQs

Specifying FASTQs

A CSV file used to indicate the input FASTQ files for libraries in a Feature Barcode experiment.

Libraries CSV

A CSV file used to indicate the molecule structure and unique Feature Barcode sequence of each feature present in the experiment.

Feature Reference CSV

A CSV files that specifies parameters required to run cellranger multi

Multi Config CSV

Custom reference

Custom Reference with mkref

Custom V(D)J Reference

Running Pipelines

Choosing a Pipeline

Computing Options

multi (3'/5'/Flex)

count (GEX + Antibody/CRISPR)

vdj (VDJ-T/B only)

Data Integration Workflows

Cell Annotation (annotate)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

QC Report

Metrics

Feature-Barcode Matrices

Molecule Info (H5)

Secondary Analysis

Cell Type Annotations

Results of aggr

Flex (Singleplex & Multiplex)

3'/5' Singleplex (GEX + VDJ + FB)

3'/5' Sample Multiplexing (GEX + VDJ + FB)

Antibody Capture

CRISPR Guide Capture

VDJ-T/B

What is Cell Ranger?

<Text as={'p'} size={'small'} weight={'medium'}>Cell Ranger v7.2 is the last version to support the analysis of LT (low throughput) libraries.</Text>

Algorithms overview

Advanced pipeline content for Cell Ranger.

Browse Q&As from the 10x Genomics support team.

View terms and definitions relevant to Single Cell products.

Access free public Chromium data from 10x Genomics.

A collection of introductions, tutorials, and blogs for data analysis beyond software.

Analysis Guides

Loupe Browser is a desktop application that allows you to interactively visualize data.