10x Genomics Support/Loupe Browser/Analysis/

Tutorials for Single Cell ATAC

Interface, Navigation, and Differential Gene Expression
Learn how to navigate the Loupe Browser interface with a pre-loaded lung carcinoma dataset and learn how to perform differential gene expression analysis.
ATAC Data Concepts
Learn some of the important concepts specific to ATAC data.
Loupe Browser for ATAC datasets
Quick overview of the tutorials and example dataset used in this series.
Identifying Cell Types
Identify cell types from known markers by examining quantitative accessibility and importing feature lists.
Identifying Cell Subtypes
Identify known immature and mature B Cell types in the dataset. This section builds on the work done in the Identifying Cell Types tutorial.
Analyze Differential Accessibility with the Peak Viewer
Using Peak Viewer to look at differential accessibility between cell subtypes.
Identify Significant Features
Identifying significant features that distinguish clusters of interest.
Share Results
Save the dataset workspace, custom clusters, and feature lists to the .cloupe.
Interoperability
Import and export projections, cluster labels, gene lists, and filters into and out of Loupe Browser.
Cell Ranger ATAC Integration
Integrating information from different output files.
Peak Viewer Details
Examining differential chromatin accessibility across genomic regions of interest.