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

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.

SUBMITTER: Parra RG 

PROVIDER: S-EPMC6755101 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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

Parra R Gonzalo RG   Papadopoulos Nikolaos N   Ahumada-Arranz Laura L   Kholtei Jakob El JE   Mottelson Noah N   Horokhovsky Yehor Y   Treutlein Barbara B   Soeding Johannes J  

Nucleic acids research 20190901 17

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  ...[more]

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