Package: dynwrap 1.2.4

Robrecht Cannoodt

dynwrap: Representing and Inferring Single-Cell Trajectories

Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Authors:Robrecht Cannoodt [aut, cre], Wouter Saelens [aut]

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NEWS

# Install 'dynwrap' in R:
install.packages('dynwrap', repos = c('https://dynverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dynverse/dynwrap/issues

Datasets:

On CRAN:

trajectory-inference

91 exports 14 stars 1.98 score 52 dependencies 1 dependents 156 scripts 525 downloads

Last updated 1 years agofrom:8525356357. Checks:OK: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 10 2024
R-4.5-winOKSep 10 2024
R-4.5-linuxOKSep 10 2024
R-4.4-winOKSep 10 2024
R-4.4-macOKSep 10 2024
R-4.3-winOKSep 10 2024
R-4.3-macERRORSep 10 2024

Exports:add_branch_trajectoryadd_cell_graphadd_cell_waypointsadd_cluster_graphadd_cyclic_trajectoryadd_dimredadd_dimred_projectionadd_end_state_probabilitiesadd_expressionadd_feature_importanceadd_groupingadd_linear_trajectoryadd_prior_informationadd_pseudotimeadd_regulatory_networkadd_rootadd_root_using_expressionadd_tde_overalladd_timing_checkpointadd_timingsadd_trajectoryadd_waypointscalculate_average_by_groupcalculate_geodesic_distancescalculate_pseudotimecalculate_trajectory_dimredclassify_milestone_networkcompute_tented_geodesic_distancesconvert_definitionconvert_milestone_percentages_to_progressionsconvert_progressions_to_milestone_percentagescreate_configcreate_docker_configcreate_singularity_configcreate_ti_method_containercreate_ti_method_definitioncreate_ti_method_rdef_authordef_containerdef_manuscriptdef_methoddef_packagedef_parametersdef_wrapperdefinitiondetermine_cell_trajectory_positionsflip_edgesgather_cells_at_milestonesgenerate_parameter_documentationgenerate_prior_informationget_default_configget_default_parametersget_dimredget_expressionget_groupingget_milestone_labellingget_ti_methodsgroup_onto_nearest_milestonesgroup_onto_trajectory_edgesinfer_trajectoriesinfer_trajectoryis_data_wrapperis_rootedis_ti_methodis_wrapper_with_dimredis_wrapper_with_expressionis_wrapper_with_feature_importanceis_wrapper_with_groupingis_wrapper_with_milestone_labellingis_wrapper_with_prior_informationis_wrapper_with_timingsis_wrapper_with_trajectoryis_wrapper_with_waypoint_cellsis_wrapper_with_waypointslabel_milestoneslabel_milestones_markersproject_milestonesproject_trajectoryproject_waypointsrandom_seedremove_rootselect_waypoint_cellsselect_waypointsset_default_configsimplify_igraph_networksimplify_trajectorytest_docker_installationtest_h5_installationtest_singularity_installationwrap_datawrap_expression

Dependencies:assertthatbabelwhalebitbit64carrierclicliprcpp11crayondescdigestdplyrdynparamdynutilsfansifsgenericsgluehmsigraphlatticelifecyclelobstrmagrittrMatrixpillarpkgconfigplyrprettyunitsprocessxprogressproxyCpspurrrR6RcppRcppArmadilloreadrremotesreshape2rlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithryaml

Creating a TI method: Container

Wouter Saelens, Robrecht Cannoodt

Rendered fromcreate_ti_method_container.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2023-03-01
Started: 2018-11-19

Creating a TI method: R

Wouter Saelens, Robrecht Cannoodt

Rendered fromcreate_ti_method_r.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2021-03-23
Started: 2018-05-31

Creating a TI method: Script

Wouter Saelens, Robrecht Cannoodt

Rendered fromcreate_ti_method_definition.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2021-03-23
Started: 2019-09-10

Creating a TI method: Wrapping trajectories

Wouter Saelens, Robrecht Cannoodt

Rendered fromcreate_ti_method_wrappers.Rmdusingknitr::rmarkdownon Sep 10 2024.

Last update: 2019-10-07
Started: 2019-03-28

Readme and manuals

Help Manual

Help pageTopics
Method process definition.method_process_definition
Add attraction of cells using RNA velocityadd_attraction
Construct a trajectory given its branch network and the pseudotime of the cells on one of the branches.add_branch_trajectory
Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.add_cell_graph
Add or select waypoint cells of a trajectoryadd_cell_waypoints determine_cell_trajectory_positions is_wrapper_with_waypoint_cells select_waypoint_cells
Constructs a trajectory using a cell grouping and a network between groups. Will use an existing grouping if it is present in the dataset.add_cluster_graph
Constructs a circular trajectory using the pseudotime values of each cell.add_cyclic_trajectory
Add or create a dimensionality reductionadd_dimred get_dimred is_wrapper_with_dimred
Constructs a trajectory by projecting cells within a dimensionality reductionadd_dimred_projection
Constructs a multifurcating trajectory using end state probabilitiesadd_end_state_probabilities
Add count and normalised expression values to a datasetadd_expression get_expression is_wrapper_with_expression
Add a feature importance to a datasetadd_feature_importance is_wrapper_with_feature_importance
Add a cell grouping to a datasetadd_grouping get_grouping is_wrapper_with_grouping
Constructs a linear trajectory using pseudotime valuesadd_linear_trajectory
Add or compute prior information for a trajectoryadd_prior_information generate_prior_information is_wrapper_with_prior_information
Add a GRN to a dynwrap objectadd_regulatory_network
Root the trajectoryadd_root add_root_using_expression is_rooted remove_root
Add information on overall differentially expressed featuresadd_tde_overall
Add timings to a trajectoryadd_timings add_timing_checkpoint is_wrapper_with_timings
Construct a trajectory given its milestone network and milestone percentages or progressionsadd_trajectory is_wrapper_with_trajectory
All allowed inputs for a TI methodallowed_inputs
All allowed outputs for a TI methodallowed_outputs
Calculate the attraction of cells to other cells using velocitycalculate_attraction
Calculate average values of a matrixcalculate_average_by_group
Calculate geodesic distances between cells in a trajectorycalculate_geodesic_distances compute_tented_geodesic_distances
Add or calculate pseudotime as distance from the rootadd_pseudotime calculate_pseudotime
Layout the trajectory and its cells in 2 dimensions using a graph layoutcalculate_trajectory_dimred
Classify a milestone networkclassify_milestone_network
Convert a definition loaded in from a yamlconvert_definition
Conversion between milestone percentages and progressionsconvert_milestone_percentages_to_progressions
Conversion between milestone percentages and progressionsconvert_progressions_to_milestone_percentages
Create a TI method from a docker / singularity containercreate_ti_method_container
Create a TI method from a local method definition filecreate_ti_method_definition
Create a TI method from an R function wrappercreate_ti_method_r
Meta information on an authordef_author
Meta information on the container in which the wrapper residesdef_container
Meta information on the manuscriptdef_manuscript
Define meta information on the TI method.def_method
Meta information on the package in which the TI function residesdef_package
Meta information on the parameters of the TI methoddef_parameters
Meta information on the wrapperdef_wrapper
Create a definitiondefinition is_ti_method
Inferring and adapting single-cell trajectoriesdynwrap
Example datasetexample_dataset
Example trajectoryexample_trajectory
Flip a set of edges of the milestone networkflip_edges
Gather cells to their closest milestonesgather_cells_at_milestones
Generate the parameter documentation of a method, use with @evalgenerate_parameter_documentation
Get the default parameters of a methodget_default_parameters
Return all TI that are installed in one or more packagesget_ti_methods
Create a grouping from a trajectorygroup_from_trajectory group_onto_nearest_milestones group_onto_trajectory_edges
Infer one or more trajectories from a single-cell datasetinfer_trajectories infer_trajectory
Label milestones either manually ('label_milestones') or using marker genes ('label_milestones_markers')get_milestone_labelling is_wrapper_with_milestone_labelling label_milestones label_milestones_markers
Metadata on prior usagesprior_usages
Metadata on priorspriors
Project a trajectory onto a dimensionality reductionproject_milestones project_trajectory
Project waypoints of a trajectory (e.g. milestones) into a space defined by cells (e.g. expression or a dimensionality reduction)project_waypoints
Generate a random seedrandom_seed
Add or create waypoints to a trajectoryadd_waypoints is_wrapper_with_waypoints select_waypoints
Simplify an igraph network such that consecutive linear edges are removedsimplify_igraph_network
Simplify a trajectory by removing transient milestonessimplify_trajectory
A DAG connecting different trajectory typestrajectory_type_dag
Metadata on the trajectory typestrajectory_types
A data wrapper for datasets and trajectoriesis_data_wrapper wrap_data
Create a wrapper object with expression and countswrap_expression
Metadata on wrapper typeswrapper_types