Cell Ranger, printed on 10/06/2022
The Chromium Single Cell Immune Profiling Software Suite is a set of analysis and visualization tools for examining 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. |
| INTRODUCTION | DOWNLOAD | TUTORIALS |
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What is Cell Ranger? What is Feature Barcode? What is High Throughput? Experimental Design |
Download Links System Requirements Installation |
V(D)J Tutorial V(D)J + Gene Expression Tutorial |
| RUNNING PIPELINES | ALGORITHMS OVERVIEW | OTHER RESOURCES |
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Generating FASTQs V(D)J T, B Cell Analysis Gene Expression Analysis Understanding V(D)J Outputs |
Gene Expression V(D)J |
References Support Questions & Answers Datasets Glossary |
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.
Loupe Browser is a visualization tool to interactively find significant genes, cell types and explore substructure in single cell data.
Loupe V(D)J Browser is an interactive visualization tool to investigate clonotypes, examine V(D)J transcripts and detect variants within clonotypes.