Extended Data Fig. 6: Scanorama worked well for 10x Genomics scRNA-seq datasets regardless of the presence of shared cell types across batches.
From: A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples
(a) t-SNE plot and (b) UMAP showing batch-effect corrections using twelve 10x Genomics scRNA-seq datasets consisting of both mixed and non-mixed samples from two sites (LLU and NCI) in different batches after Scanorama (version 1.4.) batch correction. (c) t-SNE plot and (d) UMAP showing projections of batch-effect corrections using six 10x scRNA-seq datasets consisting of only non-mixed samples from two sites (LLU and NCI) in different batches after Scanorama (version 1.4.) batch correction. Different colors represent different datasets. All the datasets were down-sampled to 1200 cells per dataset. After the batch correction, cells from the same cell line type clustered together and mixed adequately within the same cell types. All the data were preprocessed using Cell Ranger version 3.1.
