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10x Genomics
Single Cell Immune Profiling

Overview of Single Cell Immune Profiling Software

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 package includes Cell Ranger, Loupe V(D)J Browser, and Loupe Browser:

Cell Ranger

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.

INTRODUCTION DOWNLOAD TUTORIALS
What is Cell Ranger?
What is Feature Barcode?
Experimental Design
Download Links
System Requirements
Installation

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RUNNING PIPELINES ALGORITHMS OVERVIEW OTHER RESOURCES
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


Loupe Browser and Loupe V(D)J Browser

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.

INTRODUCTION DOWNLOADS TUTORIALS
What is Loupe Browser?
What is Loupe V(D)J Browser?
Download Loupe Browser
Download Loupe V(D)J Browser
Installation
Loupe V(D)J Browser
Integrated Analysis
Characterize Tumor Cells