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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  23. Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
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  26. Sampling time-dependent artifacts in single-cell genomics studies
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  35. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics
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  40. Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states
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  41. Immunology in the Era of Single-Cell Technologies
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  43. Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution
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  44. Crafting a blueprint for single-cell RNA sequencing
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  49. Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
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  55. Spatial transcriptomics reveals segregation of tumor cell states in glioblastoma and marked immunosuppression within the perinecrotic niche
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  58. Consistent RNA sequencing contamination in GTEx and other data sets
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  59. Interindividual variation in human cortical cell type abundance and expression
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  70. A spatial transcriptome map of the developing maize ear
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  74. Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified using scRNA-seq
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  75. GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing
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  77. Pancreatic Ppy-expressing γ-cells display mixed phenotypic traits and the adaptive plasticity to engage insulin production
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  81. Generating human neural diversity with a multiplexed morphogen screen in organoids
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  91. Moana: A robust and scalable cell type classification framework for single-cell RNA-Seq data
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  93. Combining single-cell RNA sequencing with spatial transcriptome analysis reveals dynamic molecular maps of cambium differentiation in the primary and secondary growth of trees
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  95. Self-recruited neutrophils trigger over-activated innate immune response and phenotypic change of cardiomyocytes in fulminant viral myocarditis
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  96. Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms
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  97. Transcriptome landscape of double negative T cells by single-cell RNA sequencing
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  99. Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis
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  100. Regulators of male and female sexual development are critical for the transmission of a malaria parasite
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