Dictionary learning for integrative, multimodal and scalable single-cell analysis

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(2), P. 293 - 304

Published: May 25, 2023

Language: Английский

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ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(3), P. 403 - 411

Published: Feb. 25, 2021

Abstract The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but outpaced development scalable software rapidly extract biological meaning from these data. Here we present a suite for analysis in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive ArchR provides an intuitive, user-focused interface complex analyses, including doublet removal, clustering cell type identification, unified peak set generation, cellular trajectory DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction multi-omic integration with RNA sequencing (scRNA-seq). Enabling over 1.2 million single cells within 8 h on standard Unix laptop, is end-to-end will accelerate understanding regulation at resolution individual cells.

Language: Английский

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Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance

Cancer Cell, Journal Year: 2020, Volume and Issue: 37(4), P. 471 - 484

Published: April 1, 2020

Language: Английский

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Genome-wide enhancer maps link risk variants to disease genes

Nature, Journal Year: 2021, Volume and Issue: 593(7858), P. 238 - 243

Published: April 7, 2021

Language: Английский

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The technological landscape and applications of single-cell multi-omics

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(10), P. 695 - 713

Published: June 6, 2023

Language: Английский

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Joint probabilistic modeling of single-cell multi-omic data with totalVI

Nature Methods, Journal Year: 2021, Volume and Issue: 18(3), P. 272 - 282

Published: Feb. 15, 2021

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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Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: April 13, 2021

Abstract The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding heterogeneity. We performed nucleus ATAC (snATAC-seq) RNA (snRNA-seq) sequencing to generate paired, cell-type-specific transcriptional profiles the adult human kidney. demonstrate that snATAC-seq is comparable snRNA-seq in assignment identity can further refine our functional heterogeneity nephron. majority differentially accessible regions are localized promoters significant proportion closely associated with expressed genes. Cell-type-specific enrichment transcription factor binding motifs implicates activation NF-κB promotes VCAM1 expression drives transition between subpopulation proximal tubule epithelial cells. Our multi-omics approach improves ability detect unique states within kidney redefines cellular thick ascending limb.

Language: Английский

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Computational principles and challenges in single-cell data integration

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(10), P. 1202 - 1215

Published: May 3, 2021

Language: Английский

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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Cell, Journal Year: 2021, Volume and Issue: 184(19), P. 5053 - 5069.e23

Published: Aug. 13, 2021

Language: Английский

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