Extended Data Fig. 4: t-SNE plots and UMAPs showing batch-effect corrections by mixability and clusterability across four scRNA-seq platforms.

t-SNE plots and UMAPs showing the batch-effect corrections performed by seven methods using 20 scRNA-seq datasets across different platforms. Datasets from 10x were down-sampled to 1200 cells per dataset. *Note, for BBKNN, only UMAP was available and shown. The scRNA-seq datasets are colored to identify the four different platforms: 10x 3´ scRNA-seq platform (red), C1 3´ HT scRNA-seq platform (yellow), C1 full-length scRNA-seq platform (light blue), and ICELL8 full-length scRNA-seq platform (dark blue). Batch correction methods included: Seurat v3.1, fastMNN (SeuratWrappers v0.1.0), Scanorama v1.4, BBKNN v1.3.5, Harmony v0.99.9, limma v3.40.4, and Combat (sva v3.32.1). Scanorama failed to separate two cell types into discrete clusters when non-10x platforms were included in the analysis. The top 2000 HVGs across all datasets were used as the gene set for batch correction. All the 10x data were preprocessed using Cell Ranger version 3.1.