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  "Title": "Longitudinal Omics Trajectory Clustering and Analysis Engine",
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  "Description": "Provides methods for estimating, classifying and comparing\nlongitudinal molecular trajectories across repeated study\nvisits using empirical, mixed-effects, generalized additive\nmodel and polynomial regression estimators. Consecutive\nmolecular changes are converted into interpretable Omics\nTrajectory Signatures (OTS) describing stable, sustained,\ntransient and rebound temporal behaviours, enabling topology-\naware clustering and consensus trajectory inference.\nLongOmicsTraj further provides a flexible query framework for\ndirectly retrieving molecular features satisfying simple or\ncomplex trajectory definitions, including multi-transition\npatterns, logical combinations of trajectory states,\ngroup-specific behaviours, and comparisons of trajectory\ntopologies across treatment arms, experimental conditions or\nother longitudinal study arms.",
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  "biocViews": "Software, TimeCourse, Transcriptomics, Clustering,\nSystemsBiology",
  "BugReports": "https://github.com/nzkermani/LongOmicsTraj/issues",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-08-04 00:18:46 UTC",
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  "Author": "Nazanin Zounemat-Kermani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-2479-3861>)",
  "Maintainer": "Nazanin Zounemat-Kermani <nonakermani@gmail.com>",
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  "_created": "2026-10-03T10:41:03.000Z",
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    "lot_plot_topology_deviation",
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    {
      "name": "lot_glucold_ots",
      "title": "GLUCOLD LongOmicsTraj object with OTS results",
      "object": "lot_glucold_ots",
      "file": "lot_glucold_ots.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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  ],
  "_help": [
    {
      "page": "compute_vmm_deltas",
      "title": "Compute adjacent visit-to-visit deltas from a Visit Mean Matrix",
      "topics": [
        "compute_vmm_deltas"
      ]
    },
    {
      "page": "LongOmicsTraj-class",
      "title": "The LongOmicsTraj Class",
      "topics": [
        "LongOmicsTraj-class"
      ]
    },
    {
      "page": "lot_cluster_purity",
      "title": "Calculate topology purity within clusters",
      "topics": [
        "lot_cluster_purity"
      ]
    },
    {
      "page": "lot_cluster_topology_score",
      "title": "Calculate a topology-aware cluster score",
      "topics": [
        "lot_cluster_topology_score"
      ]
    },
    {
      "page": "lot_compare_estimators",
      "title": "Compare trajectory estimators",
      "topics": [
        "lot_compare_estimators",
        "lot_compare_estimators,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_compute_deltas",
      "title": "Compute between-visit molecular changes",
      "topics": [
        "lot_compute_deltas",
        "lot_compute_deltas,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_compute_thresholds",
      "title": "Compute molecular-change thresholds",
      "topics": [
        "lot_compute_thresholds",
        "lot_compute_thresholds,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_consensus",
      "title": "Calculate consensus trajectory assignments",
      "topics": [
        "lot_consensus",
        "lot_consensus,DFrame-method"
      ]
    },
    {
      "page": "lot_create",
      "title": "Create a LongOmicsTraj object",
      "topics": [
        "lot_create"
      ]
    },
    {
      "page": "lot_from_clusters",
      "title": "Cluster molecular features by longitudinal trajectory",
      "topics": [
        "lot_from_clusters",
        "lot_from_clusters,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_trajectory_estimators",
      "title": "Estimate trajectories using a maSigPro-style polynomial model",
      "topics": [
        "lot_from_empirical",
        "lot_from_empirical,LongOmicsTraj-method",
        "lot_from_gam",
        "lot_from_gam,LongOmicsTraj-method",
        "lot_from_lmm",
        "lot_from_lmm,LongOmicsTraj-method",
        "lot_from_masigpro",
        "lot_from_masigpro,LongOmicsTraj-method",
        "lot_trajectory_estimators"
      ]
    },
    {
      "page": "lot_from_flexmix_clusters",
      "title": "Cluster molecular features using FlexMix trajectory models",
      "topics": [
        "lot_from_flexmix_clusters"
      ]
    },
    {
      "page": "lot_glucold",
      "title": "Cleaned longitudinal transcriptomics dataset from the GLUCOLD study",
      "topics": [
        "lot_glucold"
      ]
    },
    {
      "page": "lot_glucold_clinical",
      "title": "GLUCOLD clinical metadata",
      "topics": [
        "lot_glucold_clinical"
      ]
    },
    {
      "page": "lot_glucold_expression",
      "title": "GLUCOLD expression matrix",
      "topics": [
        "lot_glucold_expression"
      ]
    },
    {
      "page": "lot_glucold_ots",
      "title": "GLUCOLD LongOmicsTraj object with OTS results",
      "topics": [
        "lot_glucold_ots"
      ]
    },
    {
      "page": "lot_accessors",
      "title": "Access components of a LongOmicsTraj object",
      "topics": [
        "lot_accessors",
        "lot_deltas",
        "lot_deltas,LongOmicsTraj-method",
        "lot_mae",
        "lot_mae,LongOmicsTraj-method",
        "lot_ots",
        "lot_ots,LongOmicsTraj-method",
        "lot_relationships",
        "lot_relationships,LongOmicsTraj-method",
        "lot_results",
        "lot_results,LongOmicsTraj-method",
        "lot_thresholds",
        "lot_thresholds,LongOmicsTraj-method",
        "lot_vmm",
        "lot_vmm,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_map_to_ots",
      "title": "Map molecular changes to Omics Trajectory Signatures",
      "topics": [
        "lot_map_to_ots",
        "lot_map_to_ots,LongOmicsTraj-method"
      ]
    },
    {
      "page": "lot_plot_cluster_selection",
      "title": "Plot topology-aware cluster selection",
      "topics": [
        "lot_plot_cluster_selection"
      ]
    },
    {
      "page": "lot_plot_cluster_topology",
      "title": "Plot trajectory topology profiles for fitted clusters",
      "topics": [
        "lot_plot_cluster_topology"
      ]
    },
    {
      "page": "lot_plot_cluster_trajectory_arms",
      "title": "Plot trajectory arms within molecular-feature clusters",
      "topics": [
        "lot_plot_cluster_trajectory_arms"
      ]
    },
    {
      "page": "lot_plot_ots_distribution",
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