Journal
GENOME BIOLOGY
Volume 20, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-019-1663-x
Keywords
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Funding
- Helmholtz Postdoc Programme, Initiative and Networking Fund of the Helmholtz Association
- Swedish Research Council
- Wellcome
- Bloodwise
- Cancer Research UK
- NIH-NIDDK
- Wellcome-MRC Cambridge Stem Cell Institute
- Medical Research Council
- German Center for Cardiovascular Research [DZHK BER 1.2 VD]
- DFG [RA 838/5-1]
- German Research Foundation (DFG) within the Collaborative Research Centre 1243
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Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous cell transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the arising data manifold, based on estimating connectivity of manifold partitions (https://github.com/theislab/paga). PAGA maps preserve the global topology of data, allow analyzing data at different resolutions, and result in much higher computational efficiency of the typical exploratory data analysis workflow. We demonstrate the method by inferring structure-rich cell maps with consistent topology across four hematopoietic datasets, adult planaria and the zebrafish embryo and benchmark computational performance on one million neurons.
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