The single-cell transcriptional landscape of mammalian organogenesis

Nature, Journal Year: 2019, Volume and Issue: 566(7745), P. 496 - 502

Published: Feb. 20, 2019

Language: Английский

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Generalizing RNA velocity to transient cell states through dynamical modeling

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 38(12), P. 1408 - 1414

Published: Aug. 3, 2020

Language: Английский

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Current best practices in single‐cell RNA‐seq analysis: a tutorial

Molecular Systems Biology, Journal Year: 2019, Volume and Issue: 15(6)

Published: June 1, 2019

Single-cell RNA-seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single-cell analysis methods. As more tools are becoming available, it increasingly difficult navigate landscape and produce up-to-date workflow analyse one's data. Here, we detail the steps typical analysis, including pre-processing (quality control, normalization, data correction, feature selection, dimensionality reduction) cell- gene-level downstream analysis. We formulate current best-practice recommendations these based on independent comparison studies. have integrated into workflow, which apply public dataset further illustrate how work in practice. Our documented case study can found https://www.github.com/theislab/single-cell-tutorial This review will serve as tutorial new entrants field, help established users update their pipelines.

Language: Английский

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A comparison of single-cell trajectory inference methods

Nature Biotechnology, Journal Year: 2019, Volume and Issue: 37(5), P. 547 - 554

Published: April 1, 2019

Language: Английский

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PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: March 19, 2019

Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the arising data manifold, based on estimating connectivity manifold partitions ( https://github.com/theislab/paga ). PAGA maps preserve global topology data, allow analyzing at different resolutions, result in much higher computational efficiency typical exploratory analysis workflow. We demonstrate method by inferring structure-rich with consistent four hematopoietic datasets, adult planaria zebrafish embryo benchmark performance one million neurons.

Language: Английский

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Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

Cell, Journal Year: 2019, Volume and Issue: 179(4), P. 829 - 845.e20

Published: Oct. 1, 2019

Language: Английский

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Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

Cell, Journal Year: 2020, Volume and Issue: 181(2), P. 442 - 459.e29

Published: April 1, 2020

Language: Английский

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Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Cell, Journal Year: 2019, Volume and Issue: 178(3), P. 714 - 730.e22

Published: July 1, 2019

Language: Английский

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Eleven grand challenges in single-cell data science

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Feb. 7, 2020

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell technology. Thousands—or even millions—of cells analyzed a single experiment amount to data revolution biology pose unique science problems. Here, we outline eleven challenges that will be central bringing this emerging field of forward. For each challenge, highlight motivating research questions, review prior work, formulate open This compendium is for established researchers, newcomers, students alike, highlighting interesting rewarding problems the coming years.

Language: Английский

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Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

Science Advances, Journal Year: 2020, Volume and Issue: 6(28)

Published: July 8, 2020

Human lung single-cell atlas reveals the complexity and diversity of aberrant cellular populations in pulmonary fibrosis.

Language: Английский

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