Cell Ranger, printed on 04/01/2023
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.
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.
|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.|
|After June 30, 2023, new Cell Ranger releases will no longer support Targeted Gene Expression analysis.|
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?
Getting Started Tutorials
Example Data Analysis
Build a Custom Reference
Design a Custom Panel
|RUNNING PIPELINES||ALGORITHMS OVERVIEW||OTHER RESOURCES|
Targeted Gene Expression
Fixed RNA Profiling
Questions & Answers
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.
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
Downloading Output Files
Open Cloud Analysis
Supported Pipelines and Products
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.
|What is Loupe Browser?||
||Getting Started Tutorial|