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10x Genomics
Single Cell Multiome ATAC + Gene Exp.

Overview

The Single Cell Multiome ATAC + Gene Expression software suite consists of Cell Ranger ARC for the analysis and Loupe Browser for the visualization of chromatin accessibility and 3' gene expression data from the same cell produced by the 10x platform.

Cell Ranger ARC

The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells. Additionally, the pipelines perform secondary analyses like dimensionality reduction, clustering, differential analysis, and feature linkage between peaks and genes that aid in data interpretation.

INTRODUCTION DOWNLOAD TUTORIALS
What is Cell Ranger ARC?
Download Links
System Requirements
Installation

Custom Reference for Rat


RUNNING PIPELINES ALGORITHMS OVERVIEW OTHER RESOURCES
Computing Options
mkfastq
count
aggr
reanalyze
Understanding Output
Multiome ATAC + Gene Expression
Feature Linkage
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 ARC 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 TUTORIAL
What is Loupe Browser?
Download
Getting Started Tutorial