Cell Ranger, printed on 01/30/2023
The Chromium Single Cell Immune Profiling Software Suite is a set of analysis and visualization tools for examining the immune repertoire with Gene Expression and Feature Barcode data produced by the 10x Chromium Platform. The software suite includes Cell Ranger, Loupe V(D)J Browser, and Loupe Browser.
A set of analysis pipelines that perform sample demultiplexing, V(D)J transcript sequence assembly and annotation, gene expression, and Feature Barcode analysis from Single Cell Immune Profiling data.
|New in Cell Ranger v7.0: Intronic reads are counted by default for whole transcriptome gene expression data. For more information, see our recommendation on including introns for gene expression analysis page.|
What is Cell Ranger?
What is Feature Barcode?
What is Antigen Capture?
What is High Throughput?
V(D)J + Gene Expression Tutorial
|RUNNING PIPELINES||ALGORITHMS OVERVIEW||OTHER RESOURCES|
GEX, V(D)J, FB (multi) Analysis
Antigen Capture Analysis
Gene Expression Analysis
Understanding V(D)J Outputs
Understanding multi Outputs
Gene Expression |
Questions & Answers
10x Genomics Cloud is the recommended platform for running single cell pipelines for most new customers. Use your web browser to easily process FASTQ files into Cell Ranger output files. Currently available only in the United States and Canada.
What is Cloud Analysis
Creating a 10x Genomics Cloud Account
Using the 10x Genomics Cloud CLI
Uploading Files via CLI
Uploading Files via Web Browser
Uploading a Custom Reference
Downloading Output Files
Open Cloud Analysis
Supported Pipelines and Products
Loupe Browser is a visualization tool to find significant genes, cell types, and explore substructures in single cell data, interactively.
Loupe V(D)J Browser is an interactive visualization tool to investigate clonotypes, examine V(D)J transcripts and detect variants within clonotypes.
What is Loupe Browser?
What is Loupe V(D)J Browser?
Download Loupe Browser
Download Loupe V(D)J Browser
Loupe V(D)J Browser
Characterize Tumor Cells