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  "Title": "Reconstruction, visualization and analysis of branching\ntrajectories",
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  "Authors@R": "person(given=\"Daniel\", family=\"Ellwanger\", \nrole=c(\"aut\", \"cre\", \"cph\"), email=\"dc.ellwanger.dev@gmail.com\")",
  "Description": "CellTrails is an unsupervised algorithm for the de novo\nchronological ordering, visualization and analysis of\nsingle-cell expression data. CellTrails makes use of a\ngeometrically motivated concept of lower-dimensional manifold\nlearning, which exhibits a multitude of virtues that counteract\nintrinsic noise of single cell data caused by drop-outs,\ntechnical variance, and redundancy of predictive variables.\nCellTrails enables the reconstruction of branching trajectories\nand provides an intuitive graphical representation of\nexpression patterns along all branches simultaneously. It\nallows the user to define and infer the expression dynamics of\nindividual and multiple pathways towards distinct phenotypes.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:48:13 UTC",
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  "_topics": [
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  "_mentions": 1,
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  "_rbuild": "4.6.0",
  "_assets": [
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  "_realowner": "bioc",
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  "_exports": [
    "addTrail",
    "connectStates",
    "contrastTrailExpr",
    "embedSamples",
    "enrichment.test",
    "featureNames",
    "filterTrajFeaturesByCOV",
    "filterTrajFeaturesByDL",
    "filterTrajFeaturesByFF",
    "findSpectrum",
    "findStates",
    "fitDynamic",
    "fitTrajectory",
    "landmarks",
    "latentSpace",
    "latentSpace<-",
    "manifold2D",
    "manifold2D<-",
    "pca",
    "phenoNames",
    "plotDynamic",
    "plotManifold",
    "plotMap",
    "plotStateExpression",
    "plotStateSize",
    "plotStateTrajectory",
    "plotTrail",
    "plotTrajectoryFit",
    "read.ygraphml",
    "removeTrail",
    "sampleNames",
    "selectTrajectory",
    "showTrajInfo",
    "simulate_exprs",
    "states",
    "states<-",
    "stateTrajLayout<-",
    "trailNames",
    "trailNames<-",
    "trails",
    "trajComponents",
    "trajFeatureNames",
    "trajFeatureNames<-",
    "trajLayout",
    "trajLayout<-",
    "trajResiduals",
    "trajSampleNames",
    "userLandmarks",
    "userLandmarks<-",
    "write.ygraphml"
  ],
  "_datasets": [
    {
      "name": "exSCE",
      "title": "Example single-cell expression data",
      "object": "exSCE",
      "file": "exSCE.rda",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addTrail",
      "title": "ADD trail",
      "topics": [
        "addTrail",
        "addTrail,SingleCellExperiment-method"
      ]
    },
    {
      "page": "connectStates",
      "title": "Connect trajectory states",
      "topics": [
        "connectStates",
        "connectStates,SingleCellExperiment-method"
      ]
    },
    {
      "page": "contrastTrailExpr",
      "title": "Differential trail expression analysis",
      "topics": [
        "contrastTrailExpr",
        "contrastTrailExpr,SingleCellExperiment-method"
      ]
    },
    {
      "page": "embedSamples",
      "title": "Spectral embedding of biological samples",
      "topics": [
        "embedSamples",
        "embedSamples,matrix-method",
        "embedSamples,SingleCellExperiment-method"
      ]
    },
    {
      "page": "enrichment.test",
      "title": "Enrichment test",
      "topics": [
        "enrichment.test"
      ]
    },
    {
      "page": "exSCE",
      "title": "Example single-cell expression data",
      "topics": [
        "exSCE"
      ]
    },
    {
      "page": "featureNames-SingleCellExperiment-method",
      "title": "GET feature names",
      "topics": [
        "featureNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "filterTrajFeaturesByCOV",
      "title": "Filter features by Coefficient of Variation (COV)",
      "topics": [
        "filterTrajFeaturesByCOV",
        "filterTrajFeaturesByCOV,SingleCellExperiment-method"
      ]
    },
    {
      "page": "filterTrajFeaturesByDL",
      "title": "Filter trajectory features by Detection Level (DL)",
      "topics": [
        "filterTrajFeaturesByDL",
        "filterTrajFeaturesByDL,SingleCellExperiment-method"
      ]
    },
    {
      "page": "filterTrajFeaturesByFF",
      "title": "Filter features by Fano Factor",
      "topics": [
        "filterTrajFeaturesByFF",
        "filterTrajFeaturesByFF,SingleCellExperiment-method"
      ]
    },
    {
      "page": "findSpectrum",
      "title": "Determine number of informative latent dimensions",
      "topics": [
        "findSpectrum",
        "findSpectrum,numeric-method"
      ]
    },
    {
      "page": "findStates",
      "title": "Identify trajectory states",
      "topics": [
        "findStates",
        "findStates,SingleCellExperiment-method"
      ]
    },
    {
      "page": "fitDynamic",
      "title": "Fit expression dynamic",
      "topics": [
        "fitDynamic",
        "fitDynamic,SingleCellExperiment-method"
      ]
    },
    {
      "page": "fitTrajectory",
      "title": "Align samples to trajectory",
      "topics": [
        "fitTrajectory",
        "fitTrajectory,SingleCellExperiment-method"
      ]
    },
    {
      "page": "landmarks",
      "title": "GET landmarks",
      "topics": [
        "landmarks",
        "landmarks,SingleCellExperiment-method"
      ]
    },
    {
      "page": "latentSpace",
      "title": "GET CellTrails' latent space",
      "topics": [
        "latentSpace",
        "latentSpace,SingleCellExperiment-method"
      ]
    },
    {
      "page": "latentSpace-set",
      "title": "SET latent space",
      "topics": [
        "latentSpace<-",
        "latentSpace<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "manifold2D",
      "title": "GET 2D manifold representation",
      "topics": [
        "manifold2D",
        "manifold2D,SingleCellExperiment-method"
      ]
    },
    {
      "page": "manifold2D-set",
      "title": "SET 2D manifold representation",
      "topics": [
        "manifold2D<-",
        "manifold2D<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "pca",
      "title": "Principal Component Analysis",
      "topics": [
        "pca",
        "pca,SingleCellExperiment-method"
      ]
    },
    {
      "page": "phenoNames",
      "title": "GET phenotype names",
      "topics": [
        "phenoNames",
        "phenoNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotDynamic",
      "title": "Visualize dynamics",
      "topics": [
        "plotDynamic",
        "plotDynamic,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotManifold",
      "title": "Visualize the learned manifold",
      "topics": [
        "plotManifold",
        "plotManifold,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotMap",
      "title": "Visualize expression maps",
      "topics": [
        "plotMap",
        "plotMap,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotStateExpression",
      "title": "Visualize feature expression distribution per state",
      "topics": [
        "plotStateExpression",
        "plotStateExpression,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotStateSize",
      "title": "Visualize the number of samples per state",
      "topics": [
        "plotStateSize",
        "plotStateSize,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotStateTrajectory",
      "title": "Visualize state trajectory graph",
      "topics": [
        "plotStateTrajectory",
        "plotStateTrajectory,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotTrail",
      "title": "Visualize single trails",
      "topics": [
        "plotTrail",
        "plotTrail,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotTrajectoryFit",
      "title": "Visualize trajectory fit residuals",
      "topics": [
        "plotTrajectoryFit",
        "plotTrajectoryFit,SingleCellExperiment-method"
      ]
    },
    {
      "page": "read.ygraphml",
      "title": "Reads trajectory graph layout",
      "topics": [
        "read.ygraphml"
      ]
    },
    {
      "page": "removeTrail",
      "title": "REMOVE trail",
      "topics": [
        "removeTrail",
        "removeTrail,SingleCellExperiment-method"
      ]
    },
    {
      "page": "sampleNames-SingleCellExperiment-method",
      "title": "GET sample names",
      "topics": [
        "sampleNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "selectTrajectory",
      "title": "Select component from trajectory graph",
      "topics": [
        "selectTrajectory",
        "selectTrajectory,SingleCellExperiment-method"
      ]
    },
    {
      "page": "showTrajInfo",
      "title": "Shows relevant content of a SingleCellExperiment object for a CellTrails analysis",
      "topics": [
        "showTrajInfo",
        "showTrajInfo,SingleCellExperiment-method"
      ]
    },
    {
      "page": "simulate_exprs",
      "title": "Simulation of RNA-Seq expression data",
      "topics": [
        "simulate_exprs"
      ]
    },
    {
      "page": "states",
      "title": "GET states",
      "topics": [
        "states",
        "states,SingleCellExperiment-method"
      ]
    },
    {
      "page": "states-set",
      "title": "SET states",
      "topics": [
        "states<-",
        "states<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "stateTrajLayout-set",
      "title": "SET state trajectory layout",
      "topics": [
        "stateTrajLayout<-",
        "stateTrajLayout<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trailNames",
      "title": "GET trail names",
      "topics": [
        "trailNames",
        "trailNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trailNames-set",
      "title": "SET trail names",
      "topics": [
        "trailNames<-",
        "trailNames<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trails",
      "title": "GET trails",
      "topics": [
        "trails",
        "trails,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajComponents",
      "title": "GET trajectory component states",
      "topics": [
        "trajComponents",
        "trajComponents,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajFeatureNames",
      "title": "GET trajectory feature names",
      "topics": [
        "trajFeatureNames",
        "trajFeatureNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajFeatureNames-set",
      "title": "SET trajectory features by name",
      "topics": [
        "trajFeatureNames<-",
        "trajFeatureNames<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajLayout",
      "title": "GET trajectory layout",
      "topics": [
        "trajLayout",
        "trajLayout,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajLayout-set",
      "title": "SET trajectory layout",
      "topics": [
        "trajLayout<-",
        "trajLayout<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajResiduals",
      "title": "GET trajectory fitting residuals",
      "topics": [
        "trajResiduals",
        "trajResiduals,SingleCellExperiment-method"
      ]
    },
    {
      "page": "trajSampleNames",
      "title": "GET trajectory sample names",
      "topics": [
        "trajSampleNames",
        "trajSampleNames,SingleCellExperiment-method"
      ]
    },
    {
      "page": "userLandmarks",
      "title": "GET user-defined landmarks",
      "topics": [
        "userLandmarks",
        "userLandmarks,SingleCellExperiment-method"
      ]
    },
    {
      "page": "userLandmarks-set",
      "title": "SET user-defined landmarks",
      "topics": [
        "userLandmarks<-",
        "userLandmarks<-,SingleCellExperiment-method"
      ]
    },
    {
      "page": "write.ygraphml",
      "title": "Export trajectory graph",
      "topics": [
        "write.ygraphml",
        "write.ygraphml,SingleCellExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/CellTrails/raw/HEAD/README.md",
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      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "CellTrails: Reconstruction, visualization, and analysis of branching trajectories from single-cell expression data",
      "author": "Daniel Christian Ellwanger Stanford University School of Medicine Stanford, California, USA dc.ellwanger.dev@gmail.com",
      "engine": "knitr::rmarkdown",
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