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  "Package": "slingshot",
  "Title": "Tools for ordering single-cell sequencing",
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  "Description": "Provides functions for inferring continuous, branching\nlineage structures in low-dimensional data. Slingshot was\ndesigned to model developmental trajectories in single-cell RNA\nsequencing data and serve as a component in an analysis\npipeline after dimensionality reduction and clustering. It is\nflexible enough to handle arbitrarily many branching events and\nallows for the incorporation of prior knowledge through\nsupervised graph construction.",
  "Authors@R": "c(\nperson(\"Kelly\", \"Street\", email = \"street.kelly@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Davide\",\"Risso\", role = \"aut\",email = \"risso.davide@gmail.com\"),\nperson(\"Diya\",\"Das\", role = \"aut\", email = \"diyadas@berkeley.edu\"),\nperson(\"Sandrine\",\"Dudoit\", role = \"ths\", email = \"sandrine@stat.berkeley.edu\"),\nperson(\"Koen\",\"Van den Berge\", role = \"ctb\"),\nperson(\n\"Robrecht\",\n\"Cannoodt\",\nemail = \"rcannood@gmail.com\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-3641-729X\", github = \"rcannood\")\n))",
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  "biocViews": "Clustering, DifferentialExpression, GeneExpression, RNASeq,\nSequencing, Software, Sequencing, SingleCell, Transcriptomics,\nVisualization",
  "BugReports": "https://github.com/kstreet13/slingshot/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:06 UTC",
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  "Author": "Kelly Street [aut, cre, cph],\nDavide Risso [aut],\nDiya Das [aut],\nSandrine Dudoit [ths],\nKoen Van den Berge [ctb],\nRobrecht Cannoodt [ctb] (ORCID:\n<https://orcid.org/0000-0003-3641-729X>, github: rcannood)",
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        "as.PseudotimeOrdering,SingleCellExperiment-method",
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        "as.SlingshotDataSet,PseudotimeOrdering-method",
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        "as.SlingshotDataSet,SlingshotDataSet-method"
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        "embedCurves,SingleCellExperiment,character-method",
        "embedCurves,SingleCellExperiment,matrix-method"
      ]
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        "getCurves,SingleCellExperiment-method",
        "getCurves,SlingshotDataSet-method"
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        "getLineages,data.frame,ANY-method",
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        "getLineages,matrix,character-method",
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        "getLineages,SingleCellExperiment,ANY-method",
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      "topics": [
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        "newSlingshotDataSet,data.frame,ANY-method",
        "newSlingshotDataSet,matrix,ANY-method",
        "newSlingshotDataSet,matrix,character-method",
        "newSlingshotDataSet,matrix,factor-method",
        "newSlingshotDataSet,matrix,matrix-method",
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        "pairs.SlingshotDataSet"
      ]
    },
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      "title": "Plot Slingshot output",
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        "plot,SlingshotDataSet,ANY-method",
        "plot-SlingshotDataSet",
        "plot.SlingshotDataSet"
      ]
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      "topics": [
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        "plot3d.SlingshotDataSet"
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    },
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      "title": "Predict from a Slingshot model",
      "topics": [
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        "predict,SlingshotDataSet-method"
      ]
    },
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      "page": "slingBranchGraph",
      "title": "Construct graph of slingshot branch labels",
      "topics": [
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        "slingBranchGraph,ANY-method"
      ]
    },
    {
      "page": "slingBranchID",
      "title": "Get slingshot branch labels",
      "topics": [
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        "slingBranchID,ANY-method"
      ]
    },
    {
      "page": "slingClusterLabels",
      "title": "Extract cluster labels used by Slingshot",
      "topics": [
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        "slingClusterLabels,PseudotimeOrdering-method",
        "slingClusterLabels,SingleCellExperiment-method",
        "slingClusterLabels,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingCurves",
      "title": "Extract simultaneous principal curves",
      "topics": [
        "slingCurves",
        "slingCurves,PseudotimeOrdering-method",
        "slingCurves,SingleCellExperiment-method",
        "slingCurves,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingLineages",
      "title": "Extract the Slingshot lineages",
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        "slingLineages,PseudotimeOrdering-method",
        "slingLineages,SingleCellExperiment-method",
        "slingLineages,SlingshotDataSet-method"
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    {
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      "title": "Extract Slingshot minimum spanning tree",
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        "slingMST,PseudotimeOrdering-method",
        "slingMST,SingleCellExperiment-method",
        "slingMST,SlingshotDataSet-method"
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      "page": "slingParams",
      "title": "Methods for parameters used by Slingshot",
      "topics": [
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        "slingParams,PseudotimeOrdering-method",
        "slingParams,SingleCellExperiment-method",
        "slingParams,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingPseudotime",
      "title": "Get Slingshot pseudotime values",
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        "slingAvgPseudotime,ANY-method",
        "slingCurveWeights",
        "slingCurveWeights,PseudotimeOrdering-method",
        "slingCurveWeights,SingleCellExperiment-method",
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        "slingPseudotime,SingleCellExperiment-method",
        "slingPseudotime,SlingshotDataSet-method"
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    },
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      "page": "slingReducedDim",
      "title": "Extract dimensionality reduction used by Slingshot",
      "topics": [
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        "slingReducedDim,PseudotimeOrdering-method",
        "slingReducedDim,SingleCellExperiment-method",
        "slingReducedDim,SlingshotDataSet-method"
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    {
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      "title": "Perform trajectory inference with Slingshot",
      "topics": [
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        "slingshot,ClusterExperiment,ANY-method",
        "slingshot,data.frame,ANY-method",
        "slingshot,matrix,ANY-method",
        "slingshot,matrix,character-method",
        "slingshot,matrix,factor-method",
        "slingshot,matrix,matrix-method",
        "slingshot,matrix,numeric-method",
        "slingshot,SingleCellExperiment,ANY-method",
        "slingshot,SlingshotDataSet,ANY-method"
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    },
    {
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      "title": "Extract Slingshot output",
      "topics": [
        "SlingshotDataSet",
        "SlingshotDataSet,PseudotimeOrdering-method",
        "SlingshotDataSet,SingleCellExperiment-method",
        "SlingshotDataSet,SlingshotDataSet-method"
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    {
      "page": "SlingshotDataSet-class",
      "title": "Class 'SlingshotDataSet'",
      "topics": [
        "reducedDim,SlingshotDataSet,ANY-method",
        "reducedDims,SlingshotDataSet-method",
        "show,SlingshotDataSet-method",
        "SlingshotDataSet-class"
      ]
    },
    {
      "page": "slingshotExample",
      "title": "Bifurcating lineages data",
      "topics": [
        "slingshotExample"
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    }
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