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Fast Batch Alignment of Single Cell Transcriptomes Unifies Multiple Mouse Cell Atlases into an Integrated Landscape

By Jong-Eun Park, Krzysztof Polanski, Kerstin B Meyer, Sarah A Teichmann

Posted 21 Aug 2018
bioRxiv DOI: 10.1101/397042 (published DOI: 10.1093/bioinformatics/btz625)

Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. Therefore, efficient computational tools for combining diverse datasets are crucial for biology in the single cell genomics era. A number of methods have been developed to assist data integration by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration method. We illustrate the power of BBKNN for dimensionality-reduced visualisation and clustering in multiple biological scenarios, including a massive integrative study over several murine atlases. BBKNN successfully connects cell populations across experimentally heterogeneous mouse scRNA-Seq datasets, which reveals global markers of cell type and organ-specificity and provides the foundation for inferring the underlying transcription factor network. BBKNN is available at https://github.com/Teichlab/bbknn.

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