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  "Title": "Representing and Inferring Single-Cell Trajectories",
  "Description": "Provides functionality to infer trajectories from\nsingle-cell data, represent them into a common format, and\nadapt them. Other biological information can also be added,\nsuch as cellular grouping, RNA velocity and annotation. Saelens\net al. (2019) <doi:10.1038/s41587-019-0071-9>.",
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    "add_branch_trajectory",
    "add_cell_graph",
    "add_cell_waypoints",
    "add_cluster_graph",
    "add_cyclic_trajectory",
    "add_dimred",
    "add_dimred_projection",
    "add_end_state_probabilities",
    "add_expression",
    "add_feature_importance",
    "add_grouping",
    "add_linear_trajectory",
    "add_prior_information",
    "add_pseudotime",
    "add_regulatory_network",
    "add_root",
    "add_root_using_expression",
    "add_tde_overall",
    "add_timing_checkpoint",
    "add_timings",
    "add_trajectory",
    "add_waypoints",
    "calculate_average_by_group",
    "calculate_geodesic_distances",
    "calculate_pseudotime",
    "calculate_trajectory_dimred",
    "classify_milestone_network",
    "compute_tented_geodesic_distances",
    "convert_definition",
    "convert_milestone_percentages_to_progressions",
    "convert_progressions_to_milestone_percentages",
    "create_config",
    "create_docker_config",
    "create_singularity_config",
    "create_ti_method_container",
    "create_ti_method_definition",
    "create_ti_method_r",
    "def_author",
    "def_container",
    "def_manuscript",
    "def_method",
    "def_package",
    "def_parameters",
    "def_wrapper",
    "definition",
    "determine_cell_trajectory_positions",
    "flip_edges",
    "gather_cells_at_milestones",
    "generate_parameter_documentation",
    "generate_prior_information",
    "get_default_config",
    "get_default_parameters",
    "get_dimred",
    "get_expression",
    "get_grouping",
    "get_milestone_labelling",
    "get_ti_methods",
    "group_onto_nearest_milestones",
    "group_onto_trajectory_edges",
    "infer_trajectories",
    "infer_trajectory",
    "is_data_wrapper",
    "is_rooted",
    "is_ti_method",
    "is_wrapper_with_dimred",
    "is_wrapper_with_expression",
    "is_wrapper_with_feature_importance",
    "is_wrapper_with_grouping",
    "is_wrapper_with_milestone_labelling",
    "is_wrapper_with_prior_information",
    "is_wrapper_with_timings",
    "is_wrapper_with_trajectory",
    "is_wrapper_with_waypoint_cells",
    "is_wrapper_with_waypoints",
    "label_milestones",
    "label_milestones_markers",
    "project_milestones",
    "project_trajectory",
    "project_waypoints",
    "random_seed",
    "remove_root",
    "select_waypoint_cells",
    "select_waypoints",
    "set_default_config",
    "simplify_igraph_network",
    "simplify_trajectory",
    "test_docker_installation",
    "test_h5_installation",
    "test_singularity_installation",
    "wrap_data",
    "wrap_expression"
  ],
  "_datasets": [
    {
      "name": "allowed_inputs",
      "title": "All allowed inputs for a TI method",
      "object": "allowed_inputs",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "input_id",
        "description"
      ],
      "rows": 16,
      "table": true,
      "tojson": true
    },
    {
      "name": "allowed_outputs",
      "title": "All allowed outputs for a TI method",
      "object": "allowed_outputs",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "output_id",
        "description",
        "creates_trajectory",
        "required_args",
        "optional_args"
      ],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_dataset",
      "title": "Example dataset",
      "object": "example_dataset",
      "class": [
        "dynwrap::with_dimred",
        "dynwrap::with_expression",
        "dynwrap::data_wrapper",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_trajectory",
      "title": "Example trajectory",
      "object": "example_trajectory",
      "class": [
        "dynwrap::with_dimred",
        "dynwrap::with_cell_waypoints",
        "dynwrap::with_prior",
        "dynwrap::with_trajectory",
        "dynwrap::with_dimred",
        "dynwrap::with_expression",
        "dynwrap::data_wrapper",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "prior_usages",
      "title": "Metadata on prior usages",
      "object": "prior_usages",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "prior_usage",
        "color"
      ],
      "rows": 3,
      "table": true,
      "tojson": true
    },
    {
      "name": "priors",
      "title": "Metadata on priors",
      "object": "priors",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "prior_id",
        "name",
        "description",
        "type",
        "format",
        "example"
      ],
      "rows": 13,
      "table": true,
      "tojson": true
    },
    {
      "name": "trajectory_type_dag",
      "title": "A DAG connecting different trajectory types",
      "object": "trajectory_type_dag",
      "class": [
        "tbl_graph",
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "trajectory_types",
      "title": "Metadata on the trajectory types",
      "object": "trajectory_types",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "colour",
        "example_network",
        "example_nodes",
        "background_colour",
        "ancestors"
      ],
      "rows": 9,
      "table": false,
      "tojson": true
    },
    {
      "name": "wrapper_types",
      "title": "Metadata on wrapper types",
      "object": "wrapper_types",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id",
        "long_name",
        "short_name",
        "colour"
      ],
      "rows": 7,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-method_process_definition",
      "title": "Method process definition",
      "topics": [
        ".method_process_definition"
      ]
    },
    {
      "page": "add_attraction",
      "title": "Add attraction of cells using RNA velocity",
      "topics": [
        "add_attraction"
      ]
    },
    {
      "page": "add_branch_trajectory",
      "title": "Construct a trajectory given its branch network and the pseudotime of the cells on one of the branches.",
      "topics": [
        "add_branch_trajectory"
      ]
    },
    {
      "page": "add_cell_graph",
      "title": "Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.",
      "topics": [
        "add_cell_graph"
      ]
    },
    {
      "page": "add_cell_waypoints",
      "title": "Add or select waypoint cells of a trajectory",
      "topics": [
        "add_cell_waypoints",
        "determine_cell_trajectory_positions",
        "is_wrapper_with_waypoint_cells",
        "select_waypoint_cells"
      ]
    },
    {
      "page": "add_cluster_graph",
      "title": "Constructs a trajectory using a cell grouping and a network between groups. Will use an existing grouping if it is present in the dataset.",
      "topics": [
        "add_cluster_graph"
      ]
    },
    {
      "page": "add_cyclic_trajectory",
      "title": "Constructs a circular trajectory using the pseudotime values of each cell.",
      "topics": [
        "add_cyclic_trajectory"
      ]
    },
    {
      "page": "add_dimred",
      "title": "Add or create a dimensionality reduction",
      "topics": [
        "add_dimred",
        "get_dimred",
        "is_wrapper_with_dimred"
      ]
    },
    {
      "page": "add_dimred_projection",
      "title": "Constructs a trajectory by projecting cells within a dimensionality reduction",
      "topics": [
        "add_dimred_projection"
      ]
    },
    {
      "page": "add_end_state_probabilities",
      "title": "Constructs a multifurcating trajectory using end state probabilities",
      "topics": [
        "add_end_state_probabilities"
      ]
    },
    {
      "page": "add_expression",
      "title": "Add count and normalised expression values to a dataset",
      "topics": [
        "add_expression",
        "get_expression",
        "is_wrapper_with_expression"
      ]
    },
    {
      "page": "add_feature_importance",
      "title": "Add a feature importance to a dataset",
      "topics": [
        "add_feature_importance",
        "is_wrapper_with_feature_importance"
      ]
    },
    {
      "page": "add_grouping",
      "title": "Add a cell grouping to a dataset",
      "topics": [
        "add_grouping",
        "get_grouping",
        "is_wrapper_with_grouping"
      ]
    },
    {
      "page": "add_linear_trajectory",
      "title": "Constructs a linear trajectory using pseudotime values",
      "topics": [
        "add_linear_trajectory"
      ]
    },
    {
      "page": "add_prior_information",
      "title": "Add or compute prior information for a trajectory",
      "topics": [
        "add_prior_information",
        "generate_prior_information",
        "is_wrapper_with_prior_information"
      ]
    },
    {
      "page": "add_regulatory_network",
      "title": "Add a GRN to a dynwrap object",
      "topics": [
        "add_regulatory_network"
      ]
    },
    {
      "page": "add_root",
      "title": "Root the trajectory",
      "topics": [
        "add_root",
        "add_root_using_expression",
        "is_rooted",
        "remove_root"
      ]
    },
    {
      "page": "add_tde_overall",
      "title": "Add information on overall differentially expressed features",
      "topics": [
        "add_tde_overall"
      ]
    },
    {
      "page": "add_timings",
      "title": "Add timings to a trajectory",
      "topics": [
        "add_timings",
        "add_timing_checkpoint",
        "is_wrapper_with_timings"
      ]
    },
    {
      "page": "add_trajectory",
      "title": "Construct a trajectory given its milestone network and milestone percentages or progressions",
      "topics": [
        "add_trajectory",
        "is_wrapper_with_trajectory"
      ]
    },
    {
      "page": "allowed_inputs",
      "title": "All allowed inputs for a TI method",
      "topics": [
        "allowed_inputs"
      ]
    },
    {
      "page": "allowed_outputs",
      "title": "All allowed outputs for a TI method",
      "topics": [
        "allowed_outputs"
      ]
    },
    {
      "page": "calculate_attraction",
      "title": "Calculate the attraction of cells to other cells using velocity",
      "topics": [
        "calculate_attraction"
      ]
    },
    {
      "page": "calculate_average",
      "title": "Calculate average values of a matrix",
      "topics": [
        "calculate_average_by_group"
      ]
    },
    {
      "page": "calculate_geodesic_distances",
      "title": "Calculate geodesic distances between cells in a trajectory",
      "topics": [
        "calculate_geodesic_distances",
        "compute_tented_geodesic_distances"
      ]
    },
    {
      "page": "add_pseudotime",
      "title": "Add or calculate pseudotime as distance from the root",
      "topics": [
        "add_pseudotime",
        "calculate_pseudotime"
      ]
    },
    {
      "page": "calculate_trajectory_dimred",
      "title": "Layout the trajectory and its cells in 2 dimensions using a graph layout",
      "topics": [
        "calculate_trajectory_dimred"
      ]
    },
    {
      "page": "classify_milestone_network",
      "title": "Classify a milestone network",
      "topics": [
        "classify_milestone_network"
      ]
    },
    {
      "page": "convert_definition",
      "title": "Convert a definition loaded in from a yaml",
      "topics": [
        "convert_definition"
      ]
    },
    {
      "page": "convert_milestone_percentages_to_progressions",
      "title": "Conversion between milestone percentages and progressions",
      "topics": [
        "convert_milestone_percentages_to_progressions"
      ]
    },
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