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Cell Ranger


Loupe

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 software suite 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?
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
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

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.

INTRODUCTION TUTORIAL OTHER RESOURCES
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
Creating Analyses
Downloading Output Files
Transferring Projects
Billing
General FAQs
Open Cloud Analysis
Release Notes
Supported Pipelines and Products



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