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10x Genomics
Single Cell ATAC

Overview of Single Cell ATAC Software

The Chromium Single Cell ATAC Software Suite is a set of software applications for analyzing and visualizing single cell chromatin accessibility data produced by the 10x Chromium Platform. The software suite includes Cell Ranger ATAC and Loupe Browser:

Cell Ranger ATAC

Our set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.

INTRODUCTION DOWNLOAD RUNNING PIPELINES
What is Cell Ranger ATAC?
Download Links
System Requirements
Installation

Computing Options
mkfastq
count
aggr
reanalyze
Understanding Output
ALGORITHMS OVERVIEW OTHER RESOURCES
Chromatin Accessibility
Questions & Answers
Datasets



Loupe Browser

Our easy-to-use visualization software that displays peak profiles representing regions of accessible chromatin in cell clusters and differential accessibility analysis results, for interactive interrogation of Single Cell ATAC data. No programming required.

INTRODUCTION DOWNLOAD TUTORIAL
What is Loupe Browser? Differences From GEX Download Link
Installation
Getting Started Tutorial