DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

McGinnis, Christopher S., Murrow, Lyndsay M., Gartner, Zev J.·2019·Cell Systems

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  28. Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
    Squair, Jordan W., Skinnider, Michael A., Gautier, Matthieu, Foster, Leonard J., Courtine, Grégoire · 2021 · Nature Protocols
  29. Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson’s disease
    Khan, Shahzad S., Jaimon, Ebsy, Lin, Yu-En, Nikoloff, Jonas, Tonelli, Francesca, Alessi, Dario R., Pfeffer, Suzanne R. · 2024 · Proceedings of the National Academy of Sciences
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  40. Single cell dual-omic atlas of the human developing retina
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  41. Inference and effects of barcode multiplets in droplet-based single-cell assays
    Caleb A. Lareau, Sai Ma, Fabiana M. Duarte, Jason Daniel Buenrostro · 2020 · Nature Communications
  42. Brahma safeguards canalization of cardiac mesoderm differentiation
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  43. Single-cell transcriptomic analysis of neuroepithelial cells and other cell types of the gills of zebrafish (Danio rerio) exposed to hypoxia
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  47. Single-cell dissection of the human blood-brain barrier and glioma blood-tumor barrier
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  48. CXCL12+ dermal fibroblasts promote neutrophil recruitment and host defense by recognition of IL-17
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  49. The gut microbiota promotes pain in fibromyalgia
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  50. Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction
    2024
  51. Single‐Cell Sequencing Methodologies: From Transcriptome to Multi‐Dimensional Measurement
    Yingwen Chen, Jia Tao Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong James Yang · 2021 · Small Methods
  52. A human cell atlas of the pressure-induced hypertrophic heart
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  53. Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation
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  55. The single cell transcriptional landscape of esophageal adenocarcinoma and its modulation by neoadjuvant chemotherapy
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  56. An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics
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  57. A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
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  59. A multi-omics atlas of the human retina at single-cell resolution
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  60. Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles
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  63. An alternative cell cycle coordinates multiciliated cell differentiation
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  64. Epigenetic reprogramming driving successful and failed repair in acute kidney injury
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  66. Human Pancreatic Cancer Single-Cell Atlas Reveals Association of CXCL10+ Fibroblasts and Basal Subtype Tumor Cells
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  67. Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives
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  69. Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation
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  94. Multiomics profiling reveals the benefits of gamma-delta (γδ) T lymphocytes for improving the tumor microenvironment, immunotherapy efficacy and prognosis in cervical cancer
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  95. Complement and microglia activation mediate stress-induced synapse loss in layer 2/3 of the medial prefrontal cortex in male mice
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  96. Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data
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  97. Three-dimensional single-cell transcriptome imaging of thick tissues
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  98. Stomach-derived human insulin-secreting organoids restore glucose homeostasis
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  99. Single-cell analysis reveals region-heterogeneous responses in rhesus monkey spinal cord with complete injury
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  100. Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex
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