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Keywords {🔍}

cells, lineage, lineages, slingshot, curves, methods, branching, data, pseudotime, cell, inference, principal, singlecell, method, clustering, clusters, number, monocle, cluster, analysis, additional, article, mst, dataset, results, datasets, dimensionality, file, pseudotimes, reduction, values, curve, pubmed, google, scholar, multiple, single, terminal, accuracy, figure, expression, events, fig, tscan, step, average, scores, states, event, study,

Topics {✒️}

single-cell rna-seq profiles bird’s-eye view newly-developed single-cell assays single-cell rna-sequencing experiments single-cell rna-seq analysis single-cell rna-seq data single-cell rna-seq markov chain monte-carlo single-cell rna sequencing equiv \left\{\begin{array}{ll} 1 single-cell genomics data single-cell mrna quantification rna-seq experiment noisy single-cell data underlying temporal variable single-cell transcriptomics sandrine dudoit article download pdf functional genomics unit single-cell genomics full-quantile-normalized prior cell fate decisions highest-level branching events single-cell assays eventual cluster-based mst covariance-scaled euclidean distance original cell-level data rank correlation coefficient cell stem cell shape-sensitive distance measure highest-level branching event reduced-dimensionality space created reverse graph embedding stochastic mrna synthesis rna-seq bmc genomics 19 low-dimensional space obtained pearson correlation coefficient inferring cell lineages single-cell resolution privacy choices/manage cookies single-lineage hsmm dataset single-cell data quiescent stem cells gaussian mixture model wellcome open res creative commons license gaussian mixture modeling full size image minimum spanning tree

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         headline:Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
         description:Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.
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            Microarrays
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            Animal Genetics and Genomics
            Microbial Genetics and Genomics
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      headline:Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
      description:Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.
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      dateModified:2018-06-19T00:00:00Z
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         Single cell
         Lineage inference
         Pseudotime inference
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      name:Department of Molecular and Cell Biology, University of California, Berkeley, USA
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      name:Department of Statistics, University of California, Berkeley, USA
      name:Center for Computational Biology, University of California, Berkeley, USA
      name:Berkeley Institute for Data Science, University of California, Berkeley, USA

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