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  "Package": "slingshot",
  "Title": "Tools for ordering single-cell sequencing",
  "Version": "2.21.0",
  "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))",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
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  "RoxygenNote": "7.2.0",
  "Encoding": "UTF-8",
  "biocViews": "Clustering, DifferentialExpression, GeneExpression, RNASeq,\nSequencing, Software, Sequencing, SingleCell, Transcriptomics,\nVisualization",
  "BugReports": "https://github.com/kstreet13/slingshot/issues",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:06 UTC",
  "RemoteUrl": "https://github.com/bioc/slingshot",
  "RemoteRef": "HEAD",
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    "User": "root"
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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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  "_published": "2026-05-30T14:43:43.583Z",
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    "description": "Assistant Professor of Population and Public Health Sciences, Division of Biostatistics",
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    "manual.pdf"
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    "as.SlingshotDataSet",
    "embedCurves",
    "getCurves",
    "getLineages",
    "newSlingshotDataSet",
    "plot3d.SlingshotDataSet",
    "predict",
    "reducedDim",
    "reducedDims",
    "show",
    "slingAvgPseudotime",
    "slingBranchGraph",
    "slingBranchID",
    "slingClusterLabels",
    "slingCurves",
    "slingCurveWeights",
    "slingLineages",
    "slingMST",
    "slingParams",
    "slingPseudotime",
    "slingReducedDim",
    "slingshot",
    "SlingshotDataSet"
  ],
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    {
      "name": "slingshotExample",
      "title": "Bifurcating lineages data",
      "object": "slingshotExample",
      "file": "slingshotExample.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
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    {
      "page": "as.PseudotimeOrdering",
      "title": "Conversion to PseudotimeOrdering",
      "topics": [
        "as.PseudotimeOrdering",
        "as.PseudotimeOrdering,PseudotimeOrdering-method",
        "as.PseudotimeOrdering,SingleCellExperiment-method",
        "as.PseudotimeOrdering,SlingshotDataSet-method"
      ]
    },
    {
      "page": "as.SlingshotDataSet",
      "title": "Conversion to SlingshotDataSet",
      "topics": [
        "as.SlingshotDataSet",
        "as.SlingshotDataSet,PseudotimeOrdering-method",
        "as.SlingshotDataSet,SingleCellExperiment-method",
        "as.SlingshotDataSet,SlingshotDataSet-method"
      ]
    },
    {
      "page": "embedCurves",
      "title": "Embed trajectory in new space",
      "topics": [
        "embedCurves",
        "embedCurves,PseudotimeOrdering,matrix-method",
        "embedCurves,SingleCellExperiment,character-method",
        "embedCurves,SingleCellExperiment,matrix-method"
      ]
    },
    {
      "page": "getCurves",
      "title": "Construct Simultaneous Principal Curves",
      "topics": [
        "getCurves",
        "getCurves,PseudotimeOrdering-method",
        "getCurves,SingleCellExperiment-method",
        "getCurves,SlingshotDataSet-method"
      ]
    },
    {
      "page": "getLineages",
      "title": "Infer Lineage Structure from Clustered Samples",
      "topics": [
        "getLineages",
        "getLineages,data.frame,ANY-method",
        "getLineages,matrix,ANY-method",
        "getLineages,matrix,character-method",
        "getLineages,matrix,factor-method",
        "getLineages,matrix,matrix-method",
        "getLineages,matrix,numeric-method",
        "getLineages,PseudotimeOrdering,ANY-method",
        "getLineages,SingleCellExperiment,ANY-method",
        "getLineages,SlingshotDataSet,ANY-method"
      ]
    },
    {
      "page": "newSlingshotDataSet",
      "title": "Initialize an object of class 'SlingshotDataSet'",
      "topics": [
        "newSlingshotDataSet",
        "newSlingshotDataSet,data.frame,ANY-method",
        "newSlingshotDataSet,matrix,ANY-method",
        "newSlingshotDataSet,matrix,character-method",
        "newSlingshotDataSet,matrix,factor-method",
        "newSlingshotDataSet,matrix,matrix-method",
        "newSlingshotDataSet,matrix,numeric-method"
      ]
    },
    {
      "page": "pairs-SlingshotDataSet",
      "title": "Pairs plot of Slingshot output",
      "topics": [
        "pairs-SlingshotDataSet",
        "pairs.SlingshotDataSet"
      ]
    },
    {
      "page": "plot-SlingshotDataSet",
      "title": "Plot Slingshot output",
      "topics": [
        "lines.SlingshotDataSet",
        "plot,SlingshotDataSet,ANY-method",
        "plot-SlingshotDataSet",
        "plot.SlingshotDataSet"
      ]
    },
    {
      "page": "plot3d-SlingshotDataSet",
      "title": "Plot Slingshot output in 3D",
      "topics": [
        "plot3d-SlingshotDataSet",
        "plot3d.SlingshotDataSet"
      ]
    },
    {
      "page": "predict.SlingshotDataSet",
      "title": "Predict from a Slingshot model",
      "topics": [
        "predict,PseudotimeOrdering-method",
        "predict,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingBranchGraph",
      "title": "Construct graph of slingshot branch labels",
      "topics": [
        "slingBranchGraph",
        "slingBranchGraph,ANY-method"
      ]
    },
    {
      "page": "slingBranchID",
      "title": "Get slingshot branch labels",
      "topics": [
        "slingBranchID",
        "slingBranchID,ANY-method"
      ]
    },
    {
      "page": "slingClusterLabels",
      "title": "Extract cluster labels used by Slingshot",
      "topics": [
        "slingClusterLabels",
        "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",
      "topics": [
        "slingLineages",
        "slingLineages,PseudotimeOrdering-method",
        "slingLineages,SingleCellExperiment-method",
        "slingLineages,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingMST",
      "title": "Extract Slingshot minimum spanning tree",
      "topics": [
        "slingMST",
        "slingMST,PseudotimeOrdering-method",
        "slingMST,SingleCellExperiment-method",
        "slingMST,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingParams",
      "title": "Methods for parameters used by Slingshot",
      "topics": [
        "slingParams",
        "slingParams,PseudotimeOrdering-method",
        "slingParams,SingleCellExperiment-method",
        "slingParams,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingPseudotime",
      "title": "Get Slingshot pseudotime values",
      "topics": [
        "slingAvgPseudotime",
        "slingAvgPseudotime,ANY-method",
        "slingCurveWeights",
        "slingCurveWeights,PseudotimeOrdering-method",
        "slingCurveWeights,SingleCellExperiment-method",
        "slingCurveWeights,SlingshotDataSet-method",
        "slingPseudotime",
        "slingPseudotime,PseudotimeOrdering-method",
        "slingPseudotime,SingleCellExperiment-method",
        "slingPseudotime,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingReducedDim",
      "title": "Extract dimensionality reduction used by Slingshot",
      "topics": [
        "slingReducedDim",
        "slingReducedDim,PseudotimeOrdering-method",
        "slingReducedDim,SingleCellExperiment-method",
        "slingReducedDim,SlingshotDataSet-method"
      ]
    },
    {
      "page": "slingshot",
      "title": "Perform trajectory inference with Slingshot",
      "topics": [
        "slingshot",
        "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"
      ]
    },
    {
      "page": "SlingshotDataSet",
      "title": "Extract Slingshot output",
      "topics": [
        "SlingshotDataSet",
        "SlingshotDataSet,PseudotimeOrdering-method",
        "SlingshotDataSet,SingleCellExperiment-method",
        "SlingshotDataSet,SlingshotDataSet-method"
      ]
    },
    {
      "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"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/slingshot/raw/HEAD/README.md",
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      "source": "conditionsVignette.Rmd",
      "filename": "conditionsVignette.html",
      "title": "Differential Topology: Comparing Conditions along a Trajectory",
      "author": "Kelly Street and Koen Van den Berge",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Deprecation Notice",
        "Problem Statement",
        "Methods",
        "Trajectory Inference",
        "Approach 1: Distributional Differences",
        "Permutation Test",
        "Kolmogorov-Smirnov Test",
        "Approach 2: Condition Imbalance",
        "Logistic Regression",
        "Additive Logistic Regression",
        "tradeSeq-like",
        "Other Approaches",
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      "created": "2019-08-21 17:59:07",
      "modified": "2021-03-22 20:38:06",
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      "source": "vignette.Rmd",
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      "title": "Slingshot: Trajectory Inference for Single-Cell Data",
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      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview",
        "Datasets",
        "Upstream Analysis",
        "Gene Filtering",
        "Normalization",
        "Dimensionality Reduction",
        "Clustering Cells",
        "Using Slingshot",
        "Downstream Analysis",
        "Identifying temporally dynamic genes",
        "Detailed Slingshot Functionality",
        "Identifying global lineage structure",
        "Constructing smooth curves and ordering cells",
        "Running Slingshot on large datasets",
        "Multiple Trajectories",
        "Projecting Cells onto Existing Trajectories",
        "Session Info",
        "References"
      ],
      "created": "2019-04-23 21:55:37",
      "modified": "2023-03-29 18:24:20",
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