Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Feb 1;36(3):964-965.
doi: 10.1093/bioinformatics/btz625.

BBKNN: fast batch alignment of single cell transcriptomes

Krzysztof Polański  1 , Matthew D Young  1 , Zhichao Miao  1   2 , Kerstin B Meyer  1 , Sarah A Teichmann  1   3 , Jong-Eun Park  1
Affiliations

BBKNN: fast batch alignment of single cell transcriptomes

Krzysztof Polański et al. Bioinformatics. .

Abstract

Motivation: 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. A number of methods have been developed to combine diverse datasets 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 algorithm. We illustrate the power of BBKNN on large scale mouse atlasing data, and favourably benchmark its run time against a number of competing methods.

Availability and implementation: BBKNN is available at https://github.com/Teichlab/bbknn, along with documentation and multiple example notebooks, and can be installed from pip.

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

References

    1. Barkas N. et al. (2018) Wiring together large single-cell RNA-seq sample collections. bioRxiv, 460246.
    1. Butler A. et al. (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol., 36, 411.. - PMC - PubMed
    1. Büttner M. et al. (2019) A test metric for assessing single-cell RNA-seq batch correction. Nat. Methods, 16, 43.. - PubMed
    1. Dahlin J.S. et al. (2018) A single cell hematopoietic landscape resolves eight lineage trajectories and defects in kit mutant mice. Blood, 131, e1–e11. - PMC - PubMed
    1. Deng Q. et al. (2014) Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science, 343, 193–196. - PubMed

Publication types