Reconstructing complex lineage trees from scRNA-seq data using MERLoT

被引：15

作者：

Parra, R. Gonzalo ^{[1
,2
]}

Papadopoulos, Nikolaos ^{[1
]}

Ahumada-Arranz, Laura ^{[1
]}

El Kholtei, Jakob ^{[1
]}

Mottelson, Noah ^{[1
]}

Horokhovsky, Yehor ^{[1
]}

Treutlein, Barbara ^{[3
,4
]}

Soeding, Johannes ^{[1
]}

机构：

[1] Max Planck Inst Biophys Chem, Quantitat & Computat Biol Grp, Fassberg 11, D-37077 Gottingen, Germany

[2] European Mol Biol Lab, Genome Biol Unit, Meyerhofstr 1, D-69117 Heidelberg, Germany

[3] Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Deutsch Pl 6, D-04103 Leipzig, Germany

[4] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Zurich, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / 17期

关键词：

CELL FATE DECISIONS; COMMITMENT;

D O I：

10.1093/nar/gkz706

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：8961 / 8974

页数：14

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