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Cell Ranger


Loupe

10x Genomics
Single Cell Gene Expression

Overview of Single Cell Software

The Chromium Single Cell Software Suite is a set of software applications for analyzing and visualizing single cell 3’ RNA-seq Gene Expression (GEX), Targeted Gene Expression, Feature Barcode, Cell Multiplexing, and Fixed RNA Profiling, and data produced by the 10x Genomics Chromium Platform. The software suite includes Cell Ranger and Loupe Browser.

Cell Ranger

Our set of analysis pipelines perform sample demultiplexing, barcode processing, single cell 3' gene counting, and the ability to process data from Targeted Gene Expression and Feature Barcode technology.

INTRODUCTION DOWNLOAD TUTORIALS
What is Cell Ranger?
What is Feature Barcode Data?
What is Targeted GEX?
What is Cell Multiplexing?
What is LT (Low Throughput)?
What is HT (High Throughput)?
What is Fixed RNA Profiling?

Download Links
System Requirements
Installation

Getting Started Tutorials
Capturing Neutrophils
Example Data Analysis
Build a Custom Reference
Design a Custom Panel

RUNNING PIPELINES ALGORITHMS OVERVIEW OTHER RESOURCES
Choosing Pipelines
Computing Options
Troubleshooting
Understanding Outputs
Gene Expression
Targeted Gene Expression
Antibody
CRISPR
Cell Multiplexing
Fixed RNA Profiling
Questions & Answers
Datasets

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

Our easy-to-use visualization software that lets you quickly and interactively find significant genes, cell types, and substructure within your single cell data. No programming required.

INTRODUCTION DOWNLOAD TUTORIAL
What is Loupe Browser? Download Link
Tutorials