Single-cell chromatin state analysis with Signac

Nature Methods, Journal Year: 2021, Volume and Issue: 18(11), P. 1333 - 1341

Published: Nov. 1, 2021

Language: Английский

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Benchmarking atlas-level data integration in single-cell genomics

Nature Methods, Journal Year: 2021, Volume and Issue: 19(1), P. 41 - 50

Published: Dec. 23, 2021

Abstract Single-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. To guide integration method choice, we benchmarked 68 preprocessing combinations on 85 batches gene expression, chromatin accessibility simulation from 23 publications, altogether representing >1.2 million cells distributed 13 atlas-level tasks. We evaluated methods according scalability, usability their ability remove while retaining biological variation using 14 evaluation metrics. show highly variable selection improves the performance methods, whereas scaling pushes prioritize removal over conservation variation. Overall, scANVI, Scanorama, scVI scGen perform well, particularly complex tasks, single-cell ATAC-sequencing is strongly affected by choice feature space. Our freely available Python module benchmarking pipeline can identify optimal for new data, benchmark improve development.

Language: Английский

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Methods and applications for single-cell and spatial multi-omics

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 494 - 515

Published: March 2, 2023

Language: Английский

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Best practices for single-cell analysis across modalities

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 550 - 572

Published: March 31, 2023

Language: Английский

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Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(8), P. 1143 - 1155

Published: July 8, 2021

Language: Английский

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Doublet identification in single-cell sequencing data using scDblFinder

F1000Research, Journal Year: 2021, Volume and Issue: 10, P. 979 - 979

Published: Sept. 28, 2021

Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed detect them. Building on the strengths existing approaches, we developed

Language: Английский

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Spatial multi-omic map of human myocardial infarction

Nature, Journal Year: 2022, Volume and Issue: 608(7924), P. 766 - 777

Published: Aug. 10, 2022

Language: Английский

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Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(10), P. 1246 - 1258

Published: June 3, 2021

Language: Английский

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Wound healing, fibroblast heterogeneity, and fibrosis

Cell stem cell, Journal Year: 2022, Volume and Issue: 29(8), P. 1161 - 1180

Published: Aug. 1, 2022

Language: Английский

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Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(11), P. 1158 - 1168

Published: Oct. 26, 2020

Language: Английский

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