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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, and Cell Multiplexing, and data produced by the 10x 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)?

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
Computing Options
mkfastq
multi
count (Gene Expression)
count (Targeted GEX)
count (Feature Barcode)
count (Feature Barcode Only)
aggr
reanalyze
targeted-compare
targeted-depth
Understanding Output
Gene Expression
Targeted Gene Expression
Antibody
CRISPR
Cell Multiplexing
Questions & Answers
Datasets



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
Installation
Getting Started Tutorial