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Journal Article

Reconstructing complex lineage trees from scRNA-seq data using MERLoT.

MPS-Authors
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Parra,  R. G.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Papadopoulos,  N.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Ahumada-Arranz,  L.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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El Kholtei,  J.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Mottelson,  N.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Horokhovsky,  Y.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Söding,  J.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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3176961.pdf
(Publisher version), 5MB

Supplementary Material (public)

3176961_Suppl.htm
(Supplementary material), 340KB

Citation

Parra, R. G., Papadopoulos, N., Ahumada-Arranz, L., El Kholtei, J., Mottelson, N., Horokhovsky, Y., et al. (2019). Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Research, 47(17), 8961-8974. doi:10.1093/nar/gkz706.


Cite as: https://hdl.handle.net/21.11116/0000-0005-20A2-F
Abstract
Advances in single-cell transcriptomics techniques are revolutionizing studies of cellular differentiation and heterogeneity. It has become possible to track the trajectory of thousands of genes across the cellular lineage trees that represent the temporal emergence of cell types during dynamic processes. However, reconstruction of cellular lineage trees with more than a few cell fates has proved challenging. We present MERLoT (https://github.com/soedinglab/ merlot), a flexible and user-friendly tool to reconstruct complex lineage trees from single-cell transcriptomics data. It can impute temporal gene expression profiles along the reconstructed tree. We show MERLoT's capabilities on various real cases and hundreds of simulated datasets.