Extended Data Fig. 1: Benchmark of data integration.
From: An integrated transcriptomic cell atlas of human neural organoids
(a) UMAPs of HNOCA, either without any data integration (PCA) or with different data integration methods applied. Number in parenthesis indicates which level of RSS-based snapseed annotation labels were provided as input to the model for methods which support semi-supervised data integration. Dots in all UMAP embeddings, each of which represents a cell, are colored by the cell type annotation introduced in Fig. 1. a.c. = aggrecell algorithm (b) scIB benchmarking metrics on all tested integration methods. (c) PCA of the scPoli sample embeddings from the final scPoli integration of HNOCA presented throughout the manuscript, colored by publications, scRNA-seq methods, organoid protocols, protocol types, cell lines, and sample ages. (d) UMAPs of HNOCA based on the final scPoli integration, each with one data set highlighted. Here, one data set is defined as data representing one protocol in one publication. The protocol and publication of each data set are shown by the color bar and indices on top of the UMAP.
