Fig. 5
From: Assessment of computational methods for the analysis of single-cell ATAC-seq data
Benchmarking results using scATAC-seq data for 5k peripheral blood mononuclear cells (PBMCs) from 10X Genomics. a Dot plot of RAGI scores for each method, sorted by the maximum RAGI score. A positive RAGI value indicates that a method is able to produce a clustering of PBMCs in which chromatin accessibility of each marker gene is high in only a few clusters relative to the number of clusters with high accessibility of housekeeping genes. b UMAP visualization of the feature matrix produced by the top two methods (top row: SnapATAC, bottom row: chromVAR using k-mers). Chromatin accessibility of S100A12 (left, monocyte marker gene), MS4A1 (center, B cell marker gene), and GPDH (right, housekeeping gene) are projected onto the visualization. c UMAP visualization of the feature matrix produced by each method for the 5k PBMCs dataset from 10X Genomics. Individual cells are colored indicating cluster assignments using Louvain clustering