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10x Genomics
Single Cell ATAC

Overview of Single Cell ATAC Software

Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Single Cell ATAC data produced by the 10x Genomics Chromium platform.

Cell Ranger ATAC

Analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Chromium 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

Easy-to-use software for interactive visualization of Chromium Single Cell ATAC data. No programming required.

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