Back to ArchR Home
1 Getting Started with ArchR
2 Doublet Inference with ArchR
- 2.1 How does doublet identification work in ArchR?
- 2.2 Inferring scATAC-seq Doublets with ArchR
3 Creating an ArchRProject
4 Dimensionality Reduction with ArchR
5 Clustering with ArchR
- 5.1 Clustering using Seurat’s FindClusters() function
6 Single-cell Embeddings
7 Gene Scores and Marker Genes with ArchR
8 Defining Cluster Identity with scRNA-seq
9 Pseudo-bulk Replicates in ArchR
- 9.1 How Does ArchR Make Pseudo-bulk Replicates?
- 9.2 Making Pseudo-bulk Replicates
10 Calling Peaks with ArchR
11 Identifying Marker Peaks with ArchR
12 Motif and Feature Enrichment with ArchR
13 ChromVAR Deviatons Enrichment with ArchR
- 13.1 Motif Deviations
- 13.2 ArchR and Custom Deviations
14 Footprinting with ArchR
15 Integrative Analysis with ArchR
16 Trajectory Analysis with ArchR
- 16.1 Myeloid Trajectory - Monocyte Differentiation
- 16.2 Lymphoid Trajectory - B Cell Cifferentiation
17 Plot aesthetics in ArchR
18 Session Information
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ArchR: Robust and scaleable analysis of single-cell chromatin accessibility data.

Chapter 1 Getting Started with ArchR

This chapter will introduce you to how to import data into ArchR and how to create ArrowFiles, the base unit of ArchR analysis.